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Publications

A generated publication list from PubMed, enriched with Google Scholar citation counts and profile links.

Updated
2026-09-20T02:01:38Z
PI Publications
202
PI Citation Matches
199
PI Scholar
27293 citations · h-index 79
Group Unique Papers
397
Group Unique Citations
30497
This list is generated from PubMed and enriched with citation counts from Google Scholar profile data. Additional profiles: Google Scholar, DiVA, ORCID, and legacy archive.

Publication list

  1. ABAG-Rank: improving model selection of AlphaFold antibody-antigen complexes by learning to rank

    Tadiello M, Ludaic M, Viliuga V, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2026 · PMID: 42693924 · Citations: 1 · Source: pubmed

  2. Limits of deep-learning-based RNA prediction methods

    Ludaic M, Elofsson A

    Nucleic acids research · Year: 2026 · PMID: 42635124 · Citations: 9 · Source: pubmed

  3. What will be the future of computational biology for macromolecules in the era of AI?

    Elofsson A, Ben-Tal N

    PLoS computational biology · Year: 2026 · PMID: 42418429 · Citations: 1 · Source: pubmed

  4. Mass spectrometry integrates protein design into structural biology method development

    Stevens A, Osterholz H, Viliuga V, Vosselman T, Kokane S, Marklund EG, Elofsson A, Leppert A, Landreh M

    QRB discovery · Year: 2026 · PMID: 42063620 · Citations: 0 · Source: pubmed

  5. Evaluating deep learning based structure prediction methods on antibody-antigen complexes

    Fromm S, Ludaic M, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2026 · PMID: 41863324 · Citations: 23 · Source: pubmed

  6. A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins

    Rosignoli S, Taraglio S, Di Luzio F, Lustrino E, Marzella D, Elofsson A, Panella M, Paiardini A

    Bioinformatics (Oxford, England) · Year: 2026 · PMID: 41712756 · Citations: 1 · Source: pubmed

  7. Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

    Kretsch RC, Posani E, Baulin EF, Bujnicki JM, Bussi G, Cheatham TE 3rd, Chen SJ, Elofsson A, Farsani MA, Fisher ON, Gromiha MM, Gupta A, Hamada M, Harini K, Hu G, Huang D, Iwakiri J, Jain A, Kagaya Y, Kihara D, et al.

    Proteins · Year: 2026 · PMID: 41204761 · Citations: 6 · Source: pubmed

  8. AlphaFold3 at CASP16

    Elofsson A

    Proteins · Year: 2026 · PMID: 40851426 · Citations: 32 · Source: pubmed

  9. Engaging the Community: CASP Special Interest Groups

    Elofsson A, Kretsch RC, Magnus M, Montelione GT

    Proteins · Year: 2026 · PMID: 40304050 · Citations: 5 · Source: pubmed

  10. Protein Dynamics Beyond Structure Prediction

    Juliette Griffié, Sviatlana Shashkova, Antonio Ciarlo, Sreekanth K. Manikandan, Claes Andréasson, Malin Bäckström, Tristan Bereau, Hjalmar Brismar, Carlos Bustamante, Marta Carroni, Roberto Covino, Andreas Dahlin, Sebastian Deindl, Lucie Delemotte, Arne Elofsson, John Eriksson, Giovanna Fragneto, Anders Gunnarsson, Per Hammarström, Caroline Ingre, Christian Kaiser, Petronella Kettunen, Mark C. Leake, Benjamin Loos, Anna Månberg, Antonia S. J. S. Mey, Richard Neutze, Thomas Nyström, Karl Palmås, Charley Schaefer, Markus J. Tamás, Nicola Ticozzi, Tomás S. Pilvelic, Jacopo Sacquegno, B. M., Tijms, Gunnar von Heijne, Björn Wallner, Vitali Zhaunerchyk, Simon Olsson, Joana B. Pereira, Julia Fernandez-Rodriguez, Fredrik Westerlund, Giovanni Volpe

    arXiv preprint · Year: 2026 · Citations: 0 · Source: arxiv

  11. Predicting directional flexibility in proteins

    Vsevolod Viliuga, Leif Seute, Matteo Tadiello, Nicolas Wolf, Frauke Gräter, Arne Elofsson

    arXiv preprint · Year: 2026 · Citations: 0 · Source: arxiv

  12. AF_Cache: Efficient Pipeline for Running AlphaFold for High-Throughput Protein-Protein Interaction Prediction

    Sarah Narrowe, Arne Elofsson Claudio Mirabello

    arXiv preprint · Year: 2026 · Source: arxiv

  13. Blind prediction of complex water and ion ensembles around RNA in CASP16

    Kretsch RC, Posani E, Baulin EF, Bujnicki JM, Bussi G, Cheatham TE 3rd, Chen SJ, Elofsson A, Farsani MA, Fisher ON, Gromiha MM, Gupta A, Hamada M, Harini K, Hu G, Huang D, Iwakiri J, Jain A, Kagaya Y, Kihara D, et al.

    bioRxiv : the preprint server for biology · Year: 2025 · PMID: 41279659 · Citations: 6 · Source: pubmed

  14. Structural host-virus interactome profiling of intact infected cells

    Bogdanow B, Mühlberg L, Gruska I, Vetter B, Ruta J, Elofsson A, Wiebusch L, Liu F

    Nature communications · Year: 2025 · PMID: 40691152 · Citations: 15 · Source: pubmed

  15. Editorial overview: Sequences and topology (2025)

    Elofsson A, Kolodny R

    Current opinion in structural biology · Year: 2025 · PMID: 40602329 · Citations: 0 · Source: pubmed

  16. Unlocking protein networks with Predictomes: The SPOC advantage

    Elofsson A

    Molecular cell · Year: 2025 · PMID: 40118037 · Citations: 0 · Source: pubmed

  17. Native Mass Spectrometry Captures the Conformational Plasticity of Proteins with Low-Complexity Domains

    Osterholz H, Stevens A, Abramsson ML, Lama D, Brackmann K, Rising A, Elofsson A, Marklund EG, Deindl S, Leppert A, Landreh M

    JACS Au · Year: 2025 · PMID: 39886581 · Citations: 16 · Source: pubmed

  18. Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies

    Bogdanow B, Ruwolt M, Ruta J, Mühlberg L, Wang C, Zeng WF, Elofsson A, Liu F

    Molecular systems biology · Year: 2025 · PMID: 39653847 · Citations: 4 · Source: pubmed

  19. Reliable identification of homodimers using AlphaFold

    SN Danielsson, A Elofsson

    bioRxiv preprint · Year: 2025 · Citations: 3 · Source: biorxiv

  20. Flexibility-Conditioned Protein Structure Design with Flow Matching

    Vsevolod Viliuga, Leif Seute, Nicolas Wolf, Simon Wagner, Arne Elofsson, Jan Stühmer, Frauke Gräter

    arXiv preprint · Year: 2025 · Citations: 11 · Source: arxiv

  21. Energy-Based Flow Matching for Generating 3D Molecular Structure

    Wenyin Zhou, Christopher Iliffe Sprague, Vsevolod Viliuga, Matteo Tadiello, Arne Elofsson, Hossein Azizpour

    arXiv preprint · Year: 2025 · Citations: 10 · Source: arxiv

  22. MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2

    Chim HY, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2024 · PMID: 38781500 · Citations: 18 · Source: pubmed

  23. Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse

    Elofsson A, Han L, Bianchi E, Wright GJ, Jovine L

    eLife · Year: 2024 · PMID: 38666763 · Citations: 44 · Source: pubmed

  24. M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings

    Shenoy A, Kalakoti Y, Sundar D, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2024 · PMID: 38175787 · Citations: 38 · Source: pubmed

  25. Stable Autonomous Flow Matching

    Christopher Iliffe Sprague, Arne Elofsson, Hossein Azizpour

    arXiv preprint · Year: 2024 · Citations: 0 · Source: arxiv

  26. Opportunities for machine learning in scientific discovery

    R Vinuesa, J Rabault, H Azizpour, S Bauer, BW Brunton, A Elofsson, ...

    arXiv preprint · Year: 2024 · Citations: 7 · Source: arxiv

  27. Incorporating stability into flow matching

    CI Sprague, A Elofsson, H Azizpour

    ICML 2024 Workshop on Structured Probabilistic Inference {\&} Generative … , 2024 · Year: 2024 · Citations: 5 · Source: conference

  28. Hessian-Informed Flow Matching

    Christopher Iliffe Sprague, Arne Elofsson, Hossein Azizpour

    arXiv preprint · Year: 2024 · Citations: 0 · Source: arxiv

  29. Decoding complexity: how machine learning is redefining scientific discovery

    Ricardo Vinuesa, Paola Cinnella, Jean Rabault, Hossein Azizpour, Stefan Bauer, Bingni W. Brunton, Arne Elofsson, Elias Jarlebring, Hedvig Kjellstrom, Stefano Markidis, David Marlevi, Javier Garcia-Martinez, Steven L. Brunton

    arXiv preprint · Year: 2024 · Citations: 5 · Source: arxiv

  30. Peptide binder design with inverse folding and protein structure prediction

    Bryant P, Elofsson A

    Communications chemistry · Year: 2023 · PMID: 37880344 · Citations: 46 · Source: pubmed

  31. A STRP-ed definition of Structured Tandem Repeats in Proteins

    Monzon AM, Arrías PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Fornasari MS, Parisi G, Piovesan D, Kajava AV, Tosatto SCE

    Journal of structural biology · Year: 2023 · PMID: 37652396 · Citations: 16 · Source: pubmed

  32. The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems

    Ernits K, Saha CK, Brodiazhenko T, Chouhan B, Shenoy A, Buttress JA, Duque-Pedraza JJ, Bojar V, Nakamoto JA, Kurata T, Egorov AA, Shyrokova L, Johansson MJO, Mets T, Rustamova A, Džigurski J, Tenson T, Garcia-Pino A, Strahl H, Elofsson A, et al.

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2023 · PMID: 37556498 · Citations: 54 · Source: pubmed

  33. Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes

    Zhu W, Shenoy A, Kundrotas P, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2023 · PMID: 37405868 · Citations: 263 · Source: pubmed

  34. Multiplexed selectivity screening of anti-GPCR antibodies

    Dahl L, Kotliar IB, Bendes A, Dodig-Crnković T, Fromm S, Elofsson A, Uhlén M, Sakmar TP, Schwenk JM

    Science advances · Year: 2023 · PMID: 37134173 · Citations: 28 · Source: pubmed

  35. Progress at protein structure prediction, as seen in CASP15

    Elofsson A

    Current opinion in structural biology · Year: 2023 · PMID: 37060758 · Citations: 132 · Source: pubmed

  36. Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins

    Kahle M, Appelgren S, Elofsson A, Carroni M, Ädelroth P

    BMC biology · Year: 2023 · PMID: 36855050 · Citations: 11 · Source: pubmed

  37. A "grappling hook" interaction connects self-assembly and chaperone activity of Nucleophosmin 1

    Saluri M, Leppert A, Gese GV, Sahin C, Lama D, Kaldmäe M, Chen G, Elofsson A, Allison TM, Arsenian-Henriksson M, Johansson J, Lane DP, Hällberg BM, Landreh M

    PNAS nexus · Year: 2023 · PMID: 36743470 · Citations: 23 · Source: pubmed

  38. AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network

    Kang Y, Elofsson A, Jiang Y, Huang W, Yu M, Li Z

    Bioinformatics (Oxford, England) · Year: 2023 · PMID: 36692145 · Citations: 45 · Source: pubmed

  39. Towards a structurally resolved human protein interaction network

    Burke DF, Bryant P, Barrio-Hernandez I, Memon D, Pozzati G, Shenoy A, Zhu W, Dunham AS, Albanese P, Keller A, Scheltema RA, Bruce JE, Leitner A, Kundrotas P, Beltrao P, Elofsson A

    Nature structural & molecular biology · Year: 2023 · PMID: 36690744 · Citations: 2 · Source: pubmed

  40. A structural biology community assessment of AlphaFold2 applications

    Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, et al.

    Nature structural & molecular biology · Year: 2022 · PMID: 36344848 · Citations: 822 · Source: pubmed

  41. Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

    Bryant P, Pozzati G, Zhu W, Shenoy A, Kundrotas P, Elofsson A

    Nature communications · Year: 2022 · PMID: 36224222 · Citations: 0 · Source: pubmed

  42. Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones

    Österlund N, Vosselman T, Leppert A, Gräslund A, Jörnvall H, Ilag LL, Marklund EG, Elofsson A, Johansson J, Sahin C, Landreh M

    Molecular & cellular proteomics : MCP · Year: 2022 · PMID: 36115577 · Citations: 10 · Source: pubmed

  43. Complementing machine learning-based structure predictions with native mass spectrometry

    Allison TM, Degiacomi MT, Marklund EG, Jovine L, Elofsson A, Benesch JLP, Landreh M

    Protein science : a publication of the Protein Society · Year: 2022 · PMID: 35634779 · Citations: 24 · Source: pubmed

  44. Author Correction: Improved prediction of protein-protein interactions using AlphaFold2

    Bryant P, Pozzati G, Elofsson A

    Nature communications · Year: 2022 · PMID: 35332153 · Citations: 38 · Source: pubmed

  45. Improved prediction of protein-protein interactions using AlphaFold2

    Bryant P, Pozzati G, Elofsson A

    Nature communications · Year: 2022 · PMID: 35273146 · Citations: 1281 · Source: pubmed

  46. Scoring of protein-protein docking models utilizing predicted interface residues

    Pozzati G, Kundrotas P, Elofsson A

    Proteins · Year: 2022 · PMID: 35246997 · Citations: 10 · Source: pubmed

  47. The relationship between ageing and changes in the human blood and brain methylomes

    Bryant P, Elofsson A

    NAR genomics and bioinformatics · Year: 2022 · PMID: 35118376 · Citations: 3 · Source: pubmed

  48. Intra-Helical Salt Bridge Contribution to Membrane Protein Insertion

    Duart G, Lamb J, Ortiz-Mateu J, Elofsson A, Mingarro I

    Journal of molecular biology · Year: 2022 · PMID: 35093395 · Citations: 15 · Source: pubmed

  49. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

    Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, et al.

    Nucleic acids research · Year: 2022 · PMID: 34850135 · Citations: 190 · Source: pubmed

  50. Limits and potential of combined folding and docking

    Pozzati G, Zhu W, Bassot C, Lamb J, Kundrotas P, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2022 · PMID: 34788800 · Citations: 29 · Source: pubmed

  51. Toward Characterising the Cellular 3D-Proteome

    Elofsson A

    Frontiers in bioinformatics · Year: 2021 · PMID: 36353353 · Citations: 5 · Source: pubmed

  52. Protein sequence-to-structure learning: Is this the end(-to-end revolution)?

    Laine E, Eismann S, Elofsson A, Grudinin S

    Proteins · Year: 2021 · PMID: 34519095 · Citations: 50 · Source: pubmed

  53. The evolutionary history of topological variations in the CPA/AT transporters

    Sudha G, Bassot C, Lamb J, Shu N, Huang Y, Elofsson A

    PLoS computational biology · Year: 2021 · PMID: 34403419 · Citations: 4 · Source: pubmed

  54. pyconsFold: a fast and easy tool for modeling and docking using distance predictions

    Lamb J, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2021 · PMID: 34240102 · Citations: 7 · Source: pubmed

  55. GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction

    Li Z, Jiang K, Qin S, Zhong Y, Elofsson A

    PLoS computational biology · Year: 2021 · PMID: 34081706 · Citations: 26 · Source: pubmed

  56. Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families

    Bassot C, Elofsson A

    PLoS computational biology · Year: 2021 · PMID: 33857128 · Citations: 9 · Source: pubmed

  57. GraphQA: protein model quality assessment using graph convolutional networks

    Baldassarre F, Menéndez Hurtado D, Elofsson A, Azizpour H

    Bioinformatics (Oxford, England) · Year: 2021 · PMID: 32780838 · Citations: 162 · Source: pubmed

  58. Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries

    Bryant P, Elofsson A

    PeerJ · Year: 2020 · PMID: 32983643 · Citations: 77 · Source: pubmed

  59. Using Micro- and Macro-Level Network Metrics Unveils Top Communicative Gene Modules in Psoriasis

    Naderi R, Saadati Mollaei H, Elofsson A, Hosseini Ashtiani S

    Genes · Year: 2020 · PMID: 32785106 · Citations: 5 · Source: pubmed

  60. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

    Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, et al.

    F1000Research · Year: 2020 · PMID: 32566135 · Citations: 18 · Source: pubmed

  61. Decomposing Structural Response Due to Sequence Changes in Protein Domains with Machine Learning

    Bryant P, Elofsson A

    Journal of molecular biology · Year: 2020 · PMID: 32485208 · Citations: 3 · Source: pubmed

  62. Protein Contact Map Prediction Based on ResNet and DenseNet

    Li Z, Lin Y, Elofsson A, Yao Y

    BioMed research international · Year: 2020 · PMID: 32337273 · Citations: 48 · Source: pubmed

  63. A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder

    Delucchi M, Schaper E, Sachenkova O, Elofsson A, Anisimova M

    Genes · Year: 2020 · PMID: 32283633 · Citations: 70 · Source: pubmed

  64. DisProt: intrinsic protein disorder annotation in 2020

    Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, et al.

    Nucleic acids research · Year: 2020 · PMID: 31713636 · Citations: 299 · Source: pubmed

  65. An intrinsically disordered proteins community for ELIXIR

    Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, et al.

    F1000Research · Year: 2019 · PMID: 31824649 · Citations: 19 · Source: pubmed

  66. Detecting sequence signals in targeting peptides using deep learning

    Almagro Armenteros JJ, Salvatore M, Emanuelsson O, Winther O, von Heijne G, Elofsson A, Nielsen H

    Life science alliance · Year: 2019 · PMID: 31570514 · Citations: 1243 · Source: pubmed

  67. Structural basis for the interaction of the chaperone Cbp3 with newly synthesized cytochrome b during mitochondrial respiratory chain assembly

    Ndi M, Masuyer G, Dawitz H, Carlström A, Michel M, Elofsson A, Rapp M, Stenmark P, Ott M

    The Journal of biological chemistry · Year: 2019 · PMID: 31537648 · Citations: 13 · Source: pubmed

  68. Why do eukaryotic proteins contain more intrinsically disordered regions?

    Basile W, Salvatore M, Bassot C, Elofsson A

    PLoS computational biology · Year: 2019 · PMID: 31329574 · Citations: 130 · Source: pubmed

  69. Estimation of model accuracy in CASP13

    Cheng J, Choe MH, Elofsson A, Han KS, Hou J, Maghrabi AHA, McGuffin LJ, Menéndez-Hurtado D, Olechnovič K, Schwede T, Studer G, Uziela K, Venclovas Č, Wallner B

    Proteins · Year: 2019 · PMID: 31265154 · Citations: 109 · Source: pubmed

  70. Using PconsC4 and PconsFold2 to Predict Protein Structure

    Bassot C, Menendez Hurtado D, Elofsson A

    Current protocols in bioinformatics · Year: 2019 · PMID: 31063641 · Citations: 7 · Source: pubmed

  71. PconsFam: An Interactive Database of Structure Predictions of Pfam Families

    Lamb J, Jarmolinska AI, Michel M, Menéndez-Hurtado D, Sulkowska JI, Elofsson A

    Journal of molecular biology · Year: 2019 · PMID: 30796988 · Citations: 17 · Source: pubmed

  72. Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

    Elofsson A, Hess B, Lindahl E, Onufriev A, van der Spoel D, Wallqvist A

    PLoS computational biology · Year: 2019 · PMID: 30653494 · Citations: 47 · Source: pubmed

  73. PconsC4: fast, accurate and hassle-free contact predictions

    Michel M, Menéndez Hurtado D, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2019 · PMID: 30590407 · Citations: 116 · Source: pubmed

  74. Improved protein model quality assessments by changing the target function

    Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A

    Proteins · Year: 2018 · PMID: 29524250 · Citations: 22 · Source: pubmed

  75. Topology of membrane proteins-predictions, limitations and variations

    Tsirigos KD, Govindarajan S, Bassot C, Västermark Å, Lamb J, Shu N, Elofsson A

    Current opinion in structural biology · Year: 2018 · PMID: 29100082 · Citations: 47 · Source: pubmed

  76. Methods for estimation of model accuracy in CASP12

    Elofsson A, Joo K, Keasar C, Lee J, Maghrabi AHA, Manavalan B, McGuffin LJ, Ménendez Hurtado D, Mirabello C, Pilstål R, Sidi T, Uziela K, Wallner B

    Proteins · Year: 2018 · PMID: 28975666 · Citations: 34 · Source: pubmed

  77. The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction

    Salvatore M, Shu N, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2018 · PMID: 28901589 · Citations: 16 · Source: pubmed

  78. Large-scale structure prediction by improved contact predictions and model quality assessment

    Michel M, Menéndez Hurtado D, Uziela K, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28881974 · Citations: 38 · Source: pubmed

  79. Predicting accurate contacts in thousands of Pfam domain families using PconsC3

    Michel M, Skwark MJ, Menéndez Hurtado D, Ekeberg M, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28535189 · Citations: 47 · Source: pubmed

  80. SubCons: a new ensemble method for improved human subcellular localization predictions

    Salvatore M, Warholm P, Shu N, Basile W, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28407043 · Citations: 34 · Source: pubmed

  81. High GC content causes orphan proteins to be intrinsically disordered

    Basile W, Sachenkova O, Light S, Elofsson A

    PLoS computational biology · Year: 2017 · PMID: 28355220 · Citations: 89 · Source: pubmed

  82. GWAR: robust analysis and meta-analysis of genome-wide association studies

    Dimou NL, Tsirigos KD, Elofsson A, Bagos PG

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28108451 · Citations: 18 · Source: pubmed

  83. ProQ3D: improved model quality assessments using deep learning

    Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2017 · PMID: 28052925 · Citations: 210 · Source: pubmed

  84. Corrigendum: DisProt 7.0: a major update of the database of disordered proteins

    Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, et al.

    Nucleic acids research · Year: 2017 · PMID: 27965415 · Source: pubmed

  85. DisProt 7.0: a major update of the database of disordered proteins

    Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, et al.

    Nucleic acids research · Year: 2017 · PMID: 27899601 · Citations: 362 · Source: pubmed

  86. ProQ3: Improved model quality assessments using Rosetta energy terms

    Uziela K, Shu N, Wallner B, Elofsson A

    Scientific reports · Year: 2016 · PMID: 27698390 · Citations: 132 · Source: pubmed

  87. PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins

    Tsirigos KD, Elofsson A, Bagos PG

    Bioinformatics (Oxford, England) · Year: 2016 · PMID: 27587687 · Citations: 104 · Source: pubmed

  88. Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins

    Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2016 · PMID: 26794316 · Citations: 97 · Source: pubmed

  89. Improved topology prediction using the terminal hydrophobic helices rule

    Peters C, Tsirigos KD, Shu N, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2016 · PMID: 26644416 · Citations: 68 · Source: pubmed

  90. Molecular architecture of the active mitochondrial protein gate

    Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen HH, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, Lithgow T, Endo T

    Science (New York, N.Y.) · Year: 2015 · PMID: 26404837 · Citations: 289 · Source: pubmed

  91. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding

    De Marothy MT, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2015 · PMID: 25970811 · Citations: 64 · Source: pubmed

  92. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

    Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A

    Nucleic acids research · Year: 2015 · PMID: 25969446 · Citations: 1101 · Source: pubmed

  93. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

    Mirzadeh K, Martínez V, Toddo S, Guntur S, Herrgård MJ, Elofsson A, Nørholm MH, Daley DO

    ACS synthetic biology · Year: 2015 · PMID: 25951437 · Citations: 76 · Source: pubmed

  94. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    Hayat S, Sander C, Marks DS, Elofsson A

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2015 · PMID: 25858953 · Citations: 68 · Source: pubmed

  95. Improved contact predictions using the recognition of protein like contact patterns

    Skwark MJ, Raimondi D, Michel M, Elofsson A

    PLoS computational biology · Year: 2014 · PMID: 25375897 · Citations: 191 · Source: pubmed

  96. PconsFold: improved contact predictions improve protein models

    Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2014 · PMID: 25161237 · Citations: 116 · Source: pubmed

  97. Orphans and new gene origination, a structural and evolutionary perspective

    Light S, Basile W, Elofsson A

    Current opinion in structural biology · Year: 2014 · PMID: 24934869 · Citations: 40 · Source: pubmed

  98. The positive inside rule is stronger when followed by a transmembrane helix

    Virkki MT, Peters C, Nilsson D, Sörensen T, Cristobal S, Wallner B, Elofsson A

    Journal of molecular biology · Year: 2014 · PMID: 24927974 · Citations: 20 · Source: pubmed

  99. Large tilts in transmembrane helices can be induced during tertiary structure formation

    Virkki M, Boekel C, Illergård K, Peters C, Shu N, Tsirigos KD, Elofsson A, von Heijne G, Nilsson I

    Journal of molecular biology · Year: 2014 · PMID: 24793448 · Citations: 13 · Source: pubmed

  100. Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core

    Virkki MT, Agrawal N, Edsbäcker E, Cristobal S, Elofsson A, Kauko A

    Protein science : a publication of the Protein Society · Year: 2014 · PMID: 24777974 · Citations: 25 · Source: pubmed

  101. Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?

    Peters C, Elofsson A

    Proteins · Year: 2014 · PMID: 24753217 · Citations: 32 · Source: pubmed

  102. Protein expansion is primarily due to indels in intrinsically disordered regions

    Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A

    Molecular biology and evolution · Year: 2013 · PMID: 24037790 · Citations: 103 · Source: pubmed

  103. PconsD: ultra rapid, accurate model quality assessment for protein structure prediction

    Skwark MJ, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2013 · PMID: 23677942 · Citations: 34 · Source: pubmed

  104. PconsC: combination of direct information methods and alignments improves contact prediction

    Skwark MJ, Abdel-Rehim A, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2013 · PMID: 23658418 · Citations: 104 · Source: pubmed

  105. The impact of splicing on protein domain architecture

    Light S, Elofsson A

    Current opinion in structural biology · Year: 2013 · PMID: 23562110 · Citations: 54 · Source: pubmed

  106. Membrane protein shaving with thermolysin can be used to evaluate topology predictors

    Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, Käll L, Elofsson A

    Proteomics · Year: 2013 · PMID: 23512833 · Citations: 15 · Source: pubmed

  107. Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins

    Light S, Sagit R, Ekman D, Elofsson A

    Biochimica et biophysica acta · Year: 2013 · PMID: 23333420 · Citations: 45 · Source: pubmed

  108. Ligand binding properties of human galanin receptors

    Jurkowski W, Yazdi S, Elofsson A

    Molecular membrane biology · Year: 2013 · PMID: 23237663 · Citations: 28 · Source: pubmed

  109. Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion

    Bañó-Polo M, Martínez-Gil L, Wallner B, Nieva JL, Elofsson A, Mingarro I

    Journal of molecular biology · Year: 2013 · PMID: 23228331 · Citations: 40 · Source: pubmed

  110. Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins

    Imai K, Hayat S, Sakiyama N, Fujita N, Tomii K, Elofsson A, Horton P

    Methods in molecular biology (Clifton, N.J.) · Year: 2013 · PMID: 23192545 · Citations: 6 · Source: pubmed

  111. Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions

    Hayat S, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2012 · PMID: 22689784 · Citations: 15 · Source: pubmed

  112. A guideline to proteome-wide α-helical membrane protein topology predictions

    Tsirigos KD, Hennerdal A, Käll L, Elofsson A

    Proteomics · Year: 2012 · PMID: 22685073 · Citations: 42 · Source: pubmed

  113. The interface of protein structure, protein biophysics, and molecular evolution

    Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, et al.

    Protein science : a publication of the Protein Society · Year: 2012 · PMID: 22528593 · Citations: 275 · Source: pubmed

  114. The evolution of filamin-a protein domain repeat perspective

    Light S, Sagit R, Ithychanda SS, Qin J, Elofsson A

    Journal of structural biology · Year: 2012 · PMID: 22414427 · Citations: 32 · Source: pubmed

  115. BOCTOPUS: improved topology prediction of transmembrane β barrel proteins

    Hayat S, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2012 · PMID: 22247276 · Citations: 100 · Source: pubmed

  116. Molecular recognition of a single sphingolipid species by a protein's transmembrane domain

    Contreras FX, Ernst AM, Haberkant P, Björkholm P, Lindahl E, Gönen B, Tischer C, Elofsson A, von Heijne G, Thiele C, Pepperkok R, Wieland F, Brügger B

    Nature · Year: 2012 · PMID: 22230960 · Citations: 451 · Source: pubmed

  117. Manipulating the genetic code for membrane protein production: what have we learnt so far?

    Nørholm MH, Light S, Virkki MT, Elofsson A, von Heijne G, Daley DO

    Biochimica et biophysica acta · Year: 2012 · PMID: 21884679 · Citations: 45 · Source: pubmed

  118. An introduction to membrane proteins

    Hedin LE, Illergård K, Elofsson A

    Journal of proteome research · Year: 2011 · PMID: 21815691 · Citations: 150 · Source: pubmed

  119. The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity

    Basmarke-Wehelie R, Sjölinder H, Jurkowski W, Elofsson A, Arnqvist A, Engstrand L, Hagner M, Wallin E, Guan N, Kuranasekera H, Aro H, Jonsson AB

    Gastroenterology · Year: 2011 · PMID: 21699774 · Citations: 14 · Source: pubmed

  120. KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2

    Shu N, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2011 · PMID: 21505030 · Citations: 10 · Source: pubmed

  121. Rapid membrane protein topology prediction

    Hennerdal A, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2011 · PMID: 21493661 · Citations: 68 · Source: pubmed

  122. Improved predictions by Pcons.net using multiple templates

    Larsson P, Skwark MJ, Wallner B, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2011 · PMID: 21149277 · Citations: 19 · Source: pubmed

  123. Why are polar residues within the membrane core evolutionary conserved?

    Illergård K, Kauko A, Elofsson A

    Proteins · Year: 2011 · PMID: 20938980 · Citations: 67 · Source: pubmed

  124. Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants

    Lima Mde F, Eloy NB, Pegoraro C, Sagit R, Rojas C, Bretz T, Vargas L, Elofsson A, de Oliveira AC, Hemerly AS, Ferreira PC

    BMC plant biology · Year: 2010 · PMID: 21087491 · Citations: 42 · Source: pubmed

  125. Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare

    Hennerdal A, Falk J, Lindahl E, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2010 · PMID: 20882639 · Citations: 23 · Source: pubmed

  126. Determining receptor-ligand interaction of human galanin receptor type 3

    Runesson J, Sollenberg UE, Jurkowski W, Yazdi S, Eriksson EE, Elofsson A, Langel U

    Neurochemistry international · Year: 2010 · PMID: 20817064 · Citations: 19 · Source: pubmed

  127. Nebulin: a study of protein repeat evolution

    Björklund AK, Light S, Sagit R, Elofsson A

    Journal of molecular biology · Year: 2010 · PMID: 20643138 · Citations: 58 · Source: pubmed

  128. MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane

    Illergård K, Callegari S, Elofsson A

    BMC bioinformatics · Year: 2010 · PMID: 20565847 · Citations: 44 · Source: pubmed

  129. Repositioning of transmembrane alpha-helices during membrane protein folding

    Kauko A, Hedin LE, Thebaud E, Cristobal S, Elofsson A, von Heijne G

    Journal of molecular biology · Year: 2010 · PMID: 20109468 · Citations: 92 · Source: pubmed

  130. Identifying and quantifying orphan protein sequences in fungi

    Ekman D, Elofsson A

    Journal of molecular biology · Year: 2010 · PMID: 19944701 · Citations: 78 · Source: pubmed

  131. Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context

    Hedin LE, Ojemalm K, Bernsel A, Hennerdal A, Illergård K, Enquist K, Kauko A, Cristobal S, von Heijne G, Lerch-Bader M, Nilsson I, Elofsson A

    Journal of molecular biology · Year: 2010 · PMID: 19931281 · Citations: 131 · Source: pubmed

  132. Assessment of global and local model quality in CASP8 using Pcons and ProQ

    Larsson P, Skwark MJ, Wallner B, Elofsson A

    Proteins · Year: 2009 · PMID: 19544566 · Citations: 87 · Source: pubmed

  133. Structure is three to ten times more conserved than sequence--a study of structural response in protein cores

    Illergård K, Ardell DH, Elofsson A

    Proteins · Year: 2009 · PMID: 19507241 · Citations: 776 · Source: pubmed

  134. TOPCONS: consensus prediction of membrane protein topology

    Bernsel A, Viklund H, Hennerdal A, Elofsson A

    Nucleic acids research · Year: 2009 · PMID: 19429891 · Citations: 652 · Source: pubmed

  135. SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology

    Viklund H, Bernsel A, Skwark M, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2008 · PMID: 18945683 · Citations: 292 · Source: pubmed

  136. Quantitative assessment of the structural bias in protein-protein interaction assays

    Björklund AK, Light S, Hedin L, Elofsson A

    Proteomics · Year: 2008 · PMID: 18924110 · Citations: 32 · Source: pubmed

  137. Arrangements in the modular evolution of proteins

    Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A

    Trends in biochemical sciences · Year: 2008 · PMID: 18656364 · Citations: 280 · Source: pubmed

  138. Coils in the membrane core are conserved and functionally important

    Kauko A, Illergård K, Elofsson A

    Journal of molecular biology · Year: 2008 · PMID: 18511074 · Citations: 45 · Source: pubmed

  139. Prediction of membrane-protein topology from first principles

    Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2008 · PMID: 18477697 · Citations: 369 · Source: pubmed

  140. OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

    Viklund H, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2008 · PMID: 18474507 · Citations: 487 · Source: pubmed

  141. Using multiple templates to improve quality of homology models in automated homology modeling

    Larsson P, Wallner B, Lindahl E, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2008 · PMID: 18441233 · Citations: 213 · Source: pubmed

  142. Estimating the length of transmembrane helices using Z-coordinate predictions

    Papaloukas C, Granseth E, Viklund H, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2008 · PMID: 18096645 · Citations: 28 · Source: pubmed

  143. Remote homology detection of integral membrane proteins using conserved sequence features

    Bernsel A, Viklund H, Elofsson A

    Proteins · Year: 2008 · PMID: 18076048 · Citations: 14 · Source: pubmed

  144. Prediction of global and local model quality in CASP7 using Pcons and ProQ

    Wallner B, Elofsson A

    Proteins · Year: 2007 · PMID: 17894353 · Citations: 122 · Source: pubmed

  145. Quantification of the elevated rate of domain rearrangements in metazoa

    Ekman D, Björklund AK, Elofsson A

    Journal of molecular biology · Year: 2007 · PMID: 17689563 · Citations: 116 · Source: pubmed

  146. Pcons.net: protein structure prediction meta server

    Wallner B, Larsson P, Elofsson A

    Nucleic acids research · Year: 2007 · PMID: 17584798 · Citations: 77 · Source: pubmed

  147. Membrane protein structure: prediction versus reality

    Elofsson A, von Heijne G

    Annual review of biochemistry · Year: 2007 · PMID: 17579561 · Citations: 330 · Source: pubmed

  148. Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia

    Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles DA

    Genome biology · Year: 2007 · PMID: 17521457 · Citations: 55 · Source: pubmed

  149. Expansion of protein domain repeats

    Björklund AK, Ekman D, Elofsson A

    PLoS computational biology · Year: 2006 · PMID: 16933986 · Citations: 312 · Source: pubmed

  150. ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins

    Granseth E, Viklund H, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2006 · PMID: 16873471 · Citations: 68 · Source: pubmed

  151. Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps

    Ohlson T, Aggarwal V, Elofsson A, MacCallum RM

    BMC bioinformatics · Year: 2006 · PMID: 16869963 · Citations: 14 · Source: pubmed

  152. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes

    Viklund H, Granseth E, Elofsson A

    Journal of molecular biology · Year: 2006 · PMID: 16860824 · Citations: 116 · Source: pubmed

  153. PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

    Amico M, Finelli M, Rossi I, Zauli A, Elofsson A, Viklund H, von Heijne G, Jones D, Krogh A, Fariselli P, Luigi Martelli P, Casadio R

    Nucleic acids research · Year: 2006 · PMID: 16844984 · Citations: 50 · Source: pubmed

  154. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?

    Ekman D, Light S, Björklund AK, Elofsson A

    Genome biology · Year: 2006 · PMID: 16780599 · Citations: 463 · Source: pubmed

  155. Identification of correct regions in protein models using structural, alignment, and consensus information

    Wallner B, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2006 · PMID: 16522791 · Citations: 240 · Source: pubmed

  156. Preferential attachment in the evolution of metabolic networks

    Light S, Kraulis P, Elofsson A

    BMC genomics · Year: 2005 · PMID: 16281983 · Citations: 102 · Source: pubmed

  157. ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins

    Ohlson T, Elofsson A

    BMC bioinformatics · Year: 2005 · PMID: 16225676 · Citations: 27 · Source: pubmed

  158. Pcons5: combining consensus, structural evaluation and fold recognition scores

    Wallner B, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2005 · PMID: 16204344 · Citations: 127 · Source: pubmed

  159. Domain rearrangements in protein evolution

    Björklund AK, Ekman D, Light S, Frey-Skött J, Elofsson A

    Journal of molecular biology · Year: 2005 · PMID: 16198373 · Citations: 247 · Source: pubmed

  160. Tertiary windowing to detect positive diversifying selection

    Berglund AC, Wallner B, Elofsson A, Liberles DA

    Journal of molecular evolution · Year: 2005 · PMID: 15883884 · Citations: 49 · Source: pubmed

  161. All are not equal: a benchmark of different homology modeling programs

    Wallner B, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2005 · PMID: 15840834 · Citations: 297 · Source: pubmed

  162. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions

    Ekman D, Björklund AK, Frey-Skött J, Elofsson A

    Journal of molecular biology · Year: 2005 · PMID: 15808866 · Citations: 305 · Source: pubmed

  163. A study of the membrane-water interface region of membrane proteins

    Granseth E, von Heijne G, Elofsson A

    Journal of molecular biology · Year: 2005 · PMID: 15663952 · Citations: 213 · Source: pubmed

  164. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods

    Ohlson T, Wallner B, Elofsson A

    Proteins · Year: 2004 · PMID: 15326603 · Citations: 133 · Source: pubmed

  165. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

    Viklund H, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2004 · PMID: 15215532 · Citations: 323 · Source: pubmed

  166. Using evolutionary information for the query and target improves fold recognition

    Wallner B, Fang H, Ohlson T, Frey-Skött J, Elofsson A

    Proteins · Year: 2004 · PMID: 14696196 · Citations: 47 · Source: pubmed

  167. LiveBench-6: large-scale automated evaluation of protein structure prediction servers

    Rychlewski L, Fischer D, Elofsson A

    Proteins · Year: 2003 · PMID: 14579344 · Citations: 86 · Source: pubmed

  168. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller

    Wallner B, Fang H, Elofsson A

    Proteins · Year: 2003 · PMID: 14579343 · Citations: 157 · Source: pubmed

  169. CAFASP3: the third critical assessment of fully automated structure prediction methods

    Fischer D, Rychlewski L, Dunbrack RL Jr, Ortiz AR, Elofsson A

    Proteins · Year: 2003 · PMID: 14579340 · Citations: 155 · Source: pubmed

  170. In silico prediction of the peroxisomal proteome in fungi, plants and animals

    Emanuelsson O, Elofsson A, von Heijne G, Cristóbal S

    Journal of molecular biology · Year: 2003 · PMID: 12823981 · Citations: 131 · Source: pubmed

  171. 3D-Jury: a simple approach to improve protein structure predictions

    Ginalski K, Elofsson A, Fischer D, Rychlewski L

    Bioinformatics (Oxford, England) · Year: 2003 · PMID: 12761065 · Citations: 931 · Source: pubmed

  172. Can correct protein models be identified?

    Wallner B, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2003 · PMID: 12717029 · Citations: 891 · Source: pubmed

  173. Prediction of MHC class I binding peptides, using SVMHC

    Dönnes P, Elofsson A

    BMC bioinformatics · Year: 2002 · PMID: 12225620 · Citations: 370 · Source: pubmed

  174. The salmon genome (and other issues in bioinformatics)

    Milchert LE, Liberles DA, Elofsson A

    Genome biology · Year: 2002 · PMID: 12184805 · Citations: 4 · Source: pubmed

  175. Improved detection of homologous membrane proteins by inclusion of information from topology predictions

    Hedman M, Deloof H, Von Heijne G, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2002 · PMID: 11847287 · Citations: 31 · Source: pubmed

  176. A study on protein sequence alignment quality

    Elofsson A

    Proteins · Year: 2002 · PMID: 11835508 · Citations: 97 · Source: pubmed

  177. LiveBench-2: large-scale automated evaluation of protein structure prediction servers

    Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

    Proteins · Year: 2001 · PMID: 11835496 · Citations: 100 · Source: pubmed

  178. CAFASP2: the second critical assessment of fully automated structure prediction methods

    Fischer D, Elofsson A, Rychlewski L, Pazos F, Valencia A, Rost B, Ortiz AR, Dunbrack RL Jr

    Proteins · Year: 2001 · PMID: 11835495 · Citations: 138 · Source: pubmed

  179. Pcons: a neural-network-based consensus predictor that improves fold recognition

    Lundström J, Rychlewski L, Bujnicki J, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2001 · PMID: 11604541 · Citations: 384 · Source: pubmed

  180. A study of quality measures for protein threading models

    Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A

    BMC bioinformatics · Year: 2001 · PMID: 11545673 · Citations: 0 · Source: pubmed

  181. Structure prediction meta server

    Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

    Bioinformatics (Oxford, England) · Year: 2001 · PMID: 11524381 · Citations: 259 · Source: pubmed

  182. LiveBench-1: continuous benchmarking of protein structure prediction servers

    Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

    Protein science : a publication of the Protein Society · Year: 2001 · PMID: 11266621 · Citations: 146 · Source: pubmed

  183. The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2

    Fischer D, Elofsson A, Rychlewski L

    Protein engineering · Year: 2000 · PMID: 11112504 · Citations: 24 · Source: pubmed

  184. MaxSub: an automated measure for the assessment of protein structure prediction quality

    Siew N, Elofsson A, Rychlewski L, Fischer D

    Bioinformatics (Oxford, England) · Year: 2000 · PMID: 11108700 · Citations: 495 · Source: pubmed

  185. Identification of related proteins on family, superfamily and fold level

    Lindahl E, Elofsson A

    Journal of molecular biology · Year: 2000 · PMID: 10623551 · Citations: 257 · Source: pubmed

  186. Study of the electrostatics treatment in molecular dynamics simulations

    Garemyr R, Elofsson A

    Proteins · Year: 1999 · PMID: 10591101 · Citations: 36 · Source: pubmed

  187. Turns in transmembrane helices: determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale

    Monné M, Nilsson I, Elofsson A, von Heijne G

    Journal of molecular biology · Year: 1999 · PMID: 10543969 · Citations: 115 · Source: pubmed

  188. CAFASP-1: critical assessment of fully automated structure prediction methods

    Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M

    Proteins · Year: 1999 · PMID: 10526371 · Citations: 235 · Source: pubmed

  189. A comparison of sequence and structure protein domain families as a basis for structural genomics

    Elofsson A, Sonnhammer EL

    Bioinformatics (Oxford, England) · Year: 1999 · PMID: 10383473 · Citations: 91 · Source: pubmed

  190. Hidden Markov models that use predicted secondary structures for fold recognition

    Hargbo J, Elofsson A

    Proteins · Year: 1999 · PMID: 10373007 · Citations: 114 · Source: pubmed

  191. Interaction of mitochondrial presequences with DnaK and mitochondrial hsp70

    Zhang XP, Elofsson A, Andreu D, Glaser E

    Journal of molecular biology · Year: 1999 · PMID: 10329135 · Citations: 30 · Source: pubmed

  192. Architecture of beta-barrel membrane proteins: analysis of trimeric porins

    Seshadri K, Garemyr R, Wallin E, von Heijne G, Elofsson A

    Protein science : a publication of the Protein Society · Year: 1998 · PMID: 9761484 · Citations: 68 · Source: pubmed

  193. Helix-helix packing in a membrane-like environment

    Mingarro I, Elofsson A, von Heijne G

    Journal of molecular biology · Year: 1997 · PMID: 9325117 · Citations: 45 · Source: pubmed

  194. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method

    Cserzö M, Wallin E, Simon I, von Heijne G, Elofsson A

    Protein engineering · Year: 1997 · PMID: 9278280 · Citations: 1397 · Source: pubmed

  195. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria

    Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Elofsson A

    Protein science : a publication of the Protein Society · Year: 1997 · PMID: 9098890 · Citations: 191 · Source: pubmed

  196. Assessing the performance of fold recognition methods by means of a comprehensive benchmark

    Fischer D, Elofsson A, Rice D, Eisenberg D

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · Year: 1996 · PMID: 9390240 · Citations: 192 · Source: pubmed

  197. A study of combined structure/sequence profiles

    Elofsson A, Fischer D, Rice DW, Le Grand SM, Eisenberg D

    Folding & design · Year: 1996 · PMID: 9080191 · Citations: 75 · Source: pubmed

  198. Local moves: an efficient algorithm for simulation of protein folding

    Elofsson A, Le Grand SM, Eisenberg D

    Proteins · Year: 1995 · PMID: 8539252 · Citations: 89 · Source: pubmed

  199. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin

    Elofsson A, Nilsson L

    Journal of molecular biology · Year: 1993 · PMID: 8411178 · Citations: 106 · Source: pubmed

  200. Site specific point mutation changes specificity: a molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions

    Elofsson A, Kulinski T, Rigler R, Nilsson L

    Proteins · Year: 1993 · PMID: 8265564 · Citations: 10 · Source: pubmed

  201. Motion of aromatic side chains, picosecond fluorescence, and internal energy transfer in Escherichia coli thioredoxin studied by site-directed mutagenesis, time-resolved fluorescence spectroscopy, and molecular dynamics simulations

    Elofsson A, Rigler R, Nilsson L, Roslund J, Krause G, Holmgren A

    Biochemistry · Year: 1991 · PMID: 1911751 · Source: pubmed

  202. Studies on somatostatin with time-resolved spectroscopy and molecular dynamics simulations

    Elofsson A, Nilsson L, Rigler R

    International journal of peptide and protein research · Year: 1990 · PMID: 1980672 · Citations: 5 · Source: pubmed

Query: "Kundrotas P" | Publications: 75 | Citation matches: 74 | Scholar | ORCID

  1. Simulation of cell-size systems at long timescales with flexible protein structures

    Yunas K, Singh A, Copeland MM, Tytarenko AM, Kundrotas PJ, Halfmann R, Kasyanov PO, Feinberg EA, Vakser IA

    bioRxiv : the preprint server for biology · Year: 2026 · PMID: 42395490 · Citations: 0

  2. Dockground: Expanding the Resource to Protein-DNA Complexes

    Collins KW, Copeland MM, Kundrotas PJ, Vakser IA

    Journal of molecular biology · Year: 2026 · PMID: 41274550 · Citations: 1

  3. Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking

    Singh A, Copeland MM, Kundrotas PJ, Vakser IA

    Proteins · Year: 2025 · PMID: 40476317 · Citations: 0

  4. GRAMMCell: Docking-based Cell Modeling Resource

    Singh A, Tytarenko AM, Ambati VK, Copeland MM, Kundrotas PJ, Kasyanov PO, Feinberg EA, Vakser IA

    Journal of molecular biology · Year: 2025 · PMID: 40133778 · Citations: 6

  5. Highly Optimized Simulation of Atomic Resolution Cell-Like Protein Environment

    Tytarenko AM, Singh A, Ambati VK, Copeland MM, Kundrotas PJ, Halfmann R, Kasyanov PO, Feinberg EA, Vakser IA

    The journal of physical chemistry. B · Year: 2025 · PMID: 40077832 · Citations: 4

  6. Dockground: The Resource Expands to Protein-RNA Interactome

    Collins KW, Copeland MM, Kundrotas PJ, Vakser IA

    Journal of molecular biology · Year: 2025 · PMID: 39956358 · Citations: 6

  7. CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes

    Collins KW, Copeland MM, Brysbaert G, Wodak SJ, Bonvin AMJJ, Kundrotas PJ, Vakser IA, Lensink MF

    Journal of molecular biology · Year: 2024 · PMID: 39237205 · Citations: 46

  8. Diffusion of proteins in crowded solutions studied by docking-based modeling

    Singh A, Kundrotas PJ, Vakser IA

    The Journal of chemical physics · Year: 2024 · PMID: 39225532 · Citations: 15

  9. GRAMM Web Server for Protein Docking

    Singh A, Copeland MM, Kundrotas PJ, Vakser IA

    Methods in molecular biology (Clifton, N.J.) · Year: 2024 · PMID: 37676594 · Citations: 153

  10. Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes

    Zhu W, Shenoy A, Kundrotas P, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2023 · PMID: 37405868 · Citations: 263

  11. Editorial: Protein recognition and associated diseases

    Gromiha MM, Kundrotas P, Marti MA, Venclovas Č, Li M

    Frontiers in bioinformatics · Year: 2023 · PMID: 37283696

  12. Towards a structurally resolved human protein interaction network

    Burke DF, Bryant P, Barrio-Hernandez I, Memon D, Pozzati G, Shenoy A, Zhu W, Dunham AS, Albanese P, Keller A, Scheltema RA, Bruce JE, Leitner A, Kundrotas P, Beltrao P, Elofsson A

    Nature structural & molecular biology · Year: 2023 · PMID: 36690744 · Citations: 2

  13. Size of the protein-protein energy funnel in crowded environment

    Jenkins NW, Kundrotas PJ, Vakser IA

    Frontiers in molecular biosciences · Year: 2022 · PMID: 36425657 · Citations: 4

  14. A structural biology community assessment of AlphaFold2 applications

    Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, et al.

    Nature structural & molecular biology · Year: 2022 · PMID: 36344848 · Citations: 822

  15. Dockground resource for protein recognition studies

    Collins KW, Copeland MM, Kotthoff I, Singh A, Kundrotas PJ, Vakser IA

    Protein science : a publication of the Protein Society · Year: 2022 · PMID: 36281025 · Citations: 0

  16. Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

    Bryant P, Pozzati G, Zhu W, Shenoy A, Kundrotas P, Elofsson A

    Nature communications · Year: 2022 · PMID: 36224222 · Citations: 0

  17. Docking-based long timescale simulation of cell-size protein systems at atomic resolution

    Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2022 · PMID: 36191203 · Citations: 24

  18. GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes

    Malladi S, Powell HR, David A, Islam SA, Copeland MM, Kundrotas PJ, Sternberg MJE, Vakser IA

    Journal of molecular biology · Year: 2022 · PMID: 35662458 · Citations: 7

  19. DOCKGROUND membrane protein-protein set

    Kotthoff I, Kundrotas PJ, Vakser IA

    PloS one · Year: 2022 · PMID: 35580077 · Citations: 3

  20. Scoring of protein-protein docking models utilizing predicted interface residues

    Pozzati G, Kundrotas P, Elofsson A

    Proteins · Year: 2022 · PMID: 35246997 · Citations: 10

  21. Dockground scoring benchmarks for protein docking

    Kotthoff I, Kundrotas PJ, Vakser IA

    Proteins · Year: 2022 · PMID: 35072956 · Citations: 6

  22. Limits and potential of combined folding and docking

    Pozzati G, Zhu W, Bassot C, Lamb J, Kundrotas P, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2022 · PMID: 34788800 · Citations: 29

  23. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

    Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, et al.

    Proteins · Year: 2021 · PMID: 34453465 · Citations: 140

  24. Structural motifs in protein cores and at protein-protein interfaces are different

    Hadarovich A, Chakravarty D, Tuzikov AV, Ben-Tal N, Kundrotas PJ, Vakser IA

    Protein science : a publication of the Protein Society · Year: 2021 · PMID: 33166001 · Citations: 9

  25. Text mining for modeling of protein complexes enhanced by machine learning

    Badal VD, Kundrotas PJ, Vakser IA

    Bioinformatics (Oxford, England) · Year: 2021 · PMID: 32960948 · Citations: 4

  26. Dockground Tool for Development and Benchmarking of Protein Docking Procedures

    Kundrotas PJ, Kotthoff I, Choi SW, Copeland MM, Vakser IA

    Methods in molecular biology (Clifton, N.J.) · Year: 2020 · PMID: 32621232 · Citations: 14

  27. Application of docking methodologies to modeled proteins

    Singh A, Dauzhenka T, Kundrotas PJ, Sternberg MJE, Vakser IA

    Proteins · Year: 2020 · PMID: 32170770 · Citations: 47

  28. How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking

    Chakravarty D, McElfresh GW, Kundrotas PJ, Vakser IA

    Proteins · Year: 2020 · PMID: 31994759 · Citations: 14

  29. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

    Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, et al.

    Proteins · Year: 2019 · PMID: 31612567 · Citations: 145

  30. Gene ontology improves template selection in comparative protein docking

    Hadarovich A, Anishchenko I, Tuzikov AV, Kundrotas PJ, Vakser IA

    Proteins · Year: 2019 · PMID: 30520123 · Citations: 3

  31. Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking

    Dauzhenka T, Kundrotas PJ, Vakser IA

    Journal of computational chemistry · Year: 2018 · PMID: 30226647 · Citations: 22

  32. Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model

    Anishchenko I, Kundrotas PJ, Vakser IA

    Biophysical journal · Year: 2018 · PMID: 30122295 · Citations: 28

  33. Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking

    Belkin S, Kundrotas PJ, Vakser IA

    Journal of computer-aided molecular design · Year: 2018 · PMID: 30003468 · Citations: 7

  34. Natural language processing in text mining for structural modeling of protein complexes

    Badal VD, Kundrotas PJ, Vakser IA

    BMC bioinformatics · Year: 2018 · PMID: 29506465 · Citations: 43

  35. Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function

    Kundrotas PJ, Anishchenko I, Badal VD, Das M, Dauzhenka T, Vakser IA

    Proteins · Year: 2018 · PMID: 28905425 · Citations: 20

  36. Dockground: A comprehensive data resource for modeling of protein complexes

    Kundrotas PJ, Anishchenko I, Dauzhenka T, Kotthoff I, Mnevets D, Copeland MM, Vakser IA

    Protein science : a publication of the Protein Society · Year: 2018 · PMID: 28891124 · Citations: 110

  37. Structural quality of unrefined models in protein docking

    Anishchenko I, Kundrotas PJ, Vakser IA

    Proteins · Year: 2017 · PMID: 27756103 · Citations: 7

  38. Modeling complexes of modeled proteins

    Anishchenko I, Kundrotas PJ, Vakser IA

    Proteins · Year: 2017 · PMID: 27701777 · Citations: 29

  39. Template-Based Modeling of Protein-RNA Interactions

    Zheng J, Kundrotas PJ, Vakser IA, Liu S

    PLoS computational biology · Year: 2016 · PMID: 27662342 · Citations: 54

  40. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

    Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, et al.

    Proteins · Year: 2016 · PMID: 27122118 · Citations: 180

  41. Text Mining for Protein Docking

    Badal VD, Kundrotas PJ, Vakser IA

    PLoS computational biology · Year: 2015 · PMID: 26650466 · Citations: 26

  42. Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource

    Kirys T, Ruvinsky AM, Singla D, Tuzikov AV, Kundrotas PJ, Vakser IA

    BMC bioinformatics · Year: 2015 · PMID: 26227548 · Citations: 19

  43. Protein models docking benchmark 2

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

    Proteins · Year: 2015 · PMID: 25712716 · Citations: 25

  44. Structural templates for comparative protein docking

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

    Proteins · Year: 2015 · PMID: 25488330 · Citations: 34

  45. Blind prediction of interfacial water positions in CAPRI

    Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, et al.

    Proteins · Year: 2014 · PMID: 24155158 · Citations: 0

  46. Protein models: the Grand Challenge of protein docking

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

    Proteins · Year: 2014 · PMID: 23934791 · Citations: 37

  47. Structural templates for modeling homodimers

    Kundrotas PJ, Vakser IA, Janin J

    Protein science : a publication of the Protein Society · Year: 2013 · PMID: 23996787 · Citations: 19

  48. Global and local structural similarity in protein-protein complexes: implications for template-based docking

    Kundrotas PJ, Vakser IA

    Proteins · Year: 2013 · PMID: 23946125 · Citations: 43

  49. Protein-protein alternative binding modes do not overlap

    Kundrotas PJ, Vakser IA

    Protein science : a publication of the Protein Society · Year: 2013 · PMID: 23775945 · Citations: 16

  50. GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions

    Kundrotas PJ, Zhu Z, Vakser IA

    Human genomics · Year: 2012 · PMID: 23245398 · Citations: 18

  51. Templates are available to model nearly all complexes of structurally characterized proteins

    Kundrotas PJ, Zhu Z, Janin J, Vakser IA

    Proceedings of the National Academy of Sciences of the United States of America · Year: 2012 · PMID: 22645367 · Citations: 235

  52. Protein docking by the interface structure similarity: how much structure is needed?

    Sinha R, Kundrotas PJ, Vakser IA

    PloS one · Year: 2012 · PMID: 22348074 · Citations: 40

  53. Docking by structural similarity at protein-protein interfaces

    Sinha R, Kundrotas PJ, Vakser IA

    Proteins · Year: 2010 · PMID: 20715056 · Citations: 1

  54. Accuracy of protein-protein binding sites in high-throughput template-based modeling

    Kundrotas PJ, Vakser IA

    PLoS computational biology · Year: 2010 · PMID: 20369011 · Citations: 51

  55. GWIDD: Genome-wide protein docking database

    Kundrotas PJ, Zhu Z, Vakser IA

    Nucleic acids research · Year: 2010 · PMID: 19900970 · Citations: 52

  56. On the electrostatic component of protein-protein binding free energy

    Talley K, Ng C, Shoppell M, Kundrotas P, Alexov E

    PMC biophysics · Year: 2008 · PMID: 19351424 · Citations: 70

  57. Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles

    Kundrotas PJ, Lensink MF, Alexov E

    International journal of biological macromolecules · Year: 2008 · PMID: 18572239 · Citations: 66

  58. Predicting 3D structures of protein-protein complexes

    Vakser IA, Kundrotas P

    Current pharmaceutical biotechnology · Year: 2008 · PMID: 18393862 · Citations: 63

  59. Predicting interacting and interfacial residues using continuous sequence segments

    Kundrotas P, Alexov E

    International journal of biological macromolecules · Year: 2007 · PMID: 17850859 · Citations: 4

  60. Optimization of electrostatic interactions in protein-protein complexes

    Brock K, Talley K, Coley K, Kundrotas P, Alexov E

    Biophysical journal · Year: 2007 · PMID: 17693468 · Citations: 70

  61. Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families

    Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E

    Journal of bioinformatics and computational biology · Year: 2007 · PMID: 17688312 · Citations: 6

  62. BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families

    Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E

    International journal of biological macromolecules · Year: 2007 · PMID: 17320167 · Citations: 1

  63. PROTCOM: searchable database of protein complexes enhanced with domain-domain structures

    Kundrotas PJ, Alexov E

    Nucleic acids research · Year: 2007 · PMID: 17071962 · Citations: 68

  64. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

    Kundrotas PJ, Alexov EG

    BMC bioinformatics · Year: 2006 · PMID: 17109752 · Citations: 63

  65. Predicting 3D structures of transient protein-protein complexes by homology

    Kundrotas PJ, Alexov E

    Biochimica et biophysica acta · Year: 2006 · PMID: 16963323 · Citations: 39

  66. Electrostatic properties of protein-protein complexes

    Kundrotas PJ, Alexov E

    Biophysical journal · Year: 2006 · PMID: 16782791 · Citations: 119

  67. Statistical studies of flexible nonhomogeneous polypeptide chains

    Kundrotas PJ

    Biomacromolecules · Year: 2005 · PMID: 16283721 · Citations: 0

  68. Charge sequence coding in statistical modeling of unfolded proteins

    Kundrotas PJ, Karshikoff A

    Biochimica et biophysica acta · Year: 2004 · PMID: 15450845 · Citations: 9

  69. Computation of the Ising partition function for two-dimensional square grids

    Häggkvist R, Rosengren A, Andrén D, Kundrotas P, Lundow PH, Markström K

    Physical review. E, Statistical, nonlinear, and soft matter physics · Year: 2004 · PMID: 15169066 · Citations: 28

  70. Modeling of denatured state for calculation of the electrostatic contribution to protein stability

    Kundrotas PJ, Karshikoff A

    Protein science : a publication of the Protein Society · Year: 2002 · PMID: 12070320 · Citations: 44

  71. Model for calculation of electrostatic interactions in unfolded proteins

    Kundrotas PJ, Karshikoff A

    Physical review. E, Statistical, nonlinear, and soft matter physics · Year: 2002 · PMID: 11800712 · Citations: 28

  72. Dynamics of oxygen ordering in the cell-doubled phase of YBa2Cu3O6+x

    Kundrotas PJ, Tornau EE, Rosengren A

    Physical review. B, Condensed matter · Year: 1996 · PMID: 9986342 · Citations: 7

  73. Phase transitions in the three-state antiferromagnetic Potts model

    Kundrotas PJ, Lapinskas S, Rosengren A

    Physical review. B, Condensed matter · Year: 1995 · PMID: 9979951 · Citations: 15

  74. Oxygen ordering and states of holes in YBa2Cu3O6+x

    Zubkus VE, Vujicic GM, Kundrotas PJ, Tatarskij VV

    Physical review. B, Condensed matter · Year: 1992 · PMID: 10000978 · Citations: 3

  75. Phase diagrams of oxygen ordering in high-temperature superconductors RBa2Cu3O7-x

    Zubkus VE, Tornau EE, Lapinskas S, Kundrotas PJ

    Physical review. B, Condensed matter · Year: 1991 · PMID: 9997133 · Citations: 0

Query: "Flores, Samuel[author]" | Publications: 35 | Citation matches: 31 | Scholar | ORCID

  1. Combining flipped-classroom and spaced-repetition learning in a master-level bioinformatics course

    Pozzati G, Flores SC

    PLoS computational biology · Year: 2025 · PMID: 40233029 · Citations: 1

  2. RNase P cleavage of pseudoknot substrates reveals differences in active site architecture that depend on residue N-1 in the 5' leader

    Kosek DM, Leal JL, Kikovska-Stojanovska E, Mao G, Wu S, Flores SC, Kirsebom LA

    RNA biology · Year: 2025 · PMID: 39831626 · Citations: 0

  3. Research Note: A deep learning method segments chicken keel bones from whole-body X-ray images

    Sallam M, Flores SC, de Koning DJ, Johnsson M

    Poultry science · Year: 2024 · PMID: 39190989 · Citations: 6

  4. Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses

    Flores SC, Malý M, Hrebík D, Plevka P, Černý J

    Nucleic acids research · Year: 2024 · PMID: 38084886 · Citations: 0

  5. Amino acid substitutions in human growth hormone affect secondary structure and receptor binding

    Rajkovic A, Kanchugal S, Abdurakhmanov E, Howard R, Wärmländer S, Erwin J, Barrera Saldaña HA, Gräslund A, Danielson H, Flores SC

    PloS one · Year: 2023 · PMID: 36952491 · Citations: 5

  6. Mining the Protein Data Bank to improve prediction of changes in protein-protein binding

    Flores SC, Alexiou A, Glaros A

    PloS one · Year: 2021 · PMID: 34727109 · Citations: 6

  7. Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of -1 Frameshifting by tRNA(Ser3)

    Caulfield T, Coban M, Tek A, Flores SC

    Biomolecules · Year: 2019 · PMID: 31752208 · Citations: 13

  8. Hospital-Level Variation in Practice Patterns and Patient Outcomes for Pediatric Patients Hospitalized With Functional Constipation

    Librizzi J, Flores S, Morse K, Kelleher K, Carter J, Bode R

    Hospital pediatrics · Year: 2017 · PMID: 28522604

  9. Insights from engineering the Affibody-Fc interaction with a computational-experimental method

    Nosrati M, Solbak S, Nordesjö O, Nissbeck M, Dourado DFAR, Andersson KG, Housaindokht MR, Löfblom J, Virtanen A, Danielson UH, Flores SC

    Protein engineering, design & selection : PEDS · Year: 2017 · PMID: 28472513 · Citations: 12

  10. Modeling and fitting protein-protein complexes to predict change of binding energy

    Dourado DF, Flores SC

    Scientific reports · Year: 2016 · PMID: 27173910 · Citations: 21

  11. MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory

    Tek A, Korostelev AA, Flores SC

    Nucleic acids research · Year: 2016 · PMID: 26673695 · Citations: 10

  12. A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate

    Koripella RK, Holm M, Dourado D, Mandava CS, Flores S, Sanyal S

    Scientific reports · Year: 2015 · PMID: 26264741 · Citations: 38

  13. Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin

    Fiesel FC, Caulfield TR, Moussaud-Lamodière EL, Ogaki K, Dourado DF, Flores SC, Ross OA, Springer W

    Human mutation · Year: 2015 · PMID: 25939424 · Citations: 98

  14. Cysteines in the neuropilin-2 MAM domain modulate receptor homooligomerization and signal transduction

    Barton R, Driscoll A, Flores S, Mudbhari D, Collins T, Iovine MK, Berger BW

    Biopolymers · Year: 2015 · PMID: 25656526

  15. Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin

    Caulfield TR, Fiesel FC, Moussaud-Lamodière EL, Dourado DF, Flores SC, Springer W

    PLoS computational biology · Year: 2014 · PMID: 25375667 · Citations: 122

  16. A multiscale approach to predicting affinity changes in protein-protein interfaces

    Dourado DF, Flores SC

    Proteins · Year: 2014 · PMID: 24975440 · Citations: 76

  17. Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome

    Flores SC

    Nucleic acids research · Year: 2014 · PMID: 24081579 · Citations: 22

  18. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

    Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, et al.

    Proteins · Year: 2013 · PMID: 23843247 · Citations: 118

  19. Insights into diseases of human telomerase from dynamical modeling

    Flores SC, Zemora G, Waldsich C

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · Year: 2013 · PMID: 23424125 · Citations: 5

  20. The use of the tracer methodology to assess the quality of care for patients enrolled in Medical Insurance for a New Generation

    Durán-Arenas L, Muñoz-Hernández O, Hernández-Ramírez Ldel C, Jasso-Gutiérrez L, Flores S, Aldaz-Rodríguez V, Zurita JM

    Salud publica de Mexico · Year: 2012 · PMID: 22965443

  21. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction

    Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, et al.

    RNA (New York, N.Y.) · Year: 2012 · PMID: 22361291 · Citations: 354

  22. Multiscale modeling of macromolecular biosystems

    Flores SC, Bernauer J, Shin S, Zhou R, Huang X

    Briefings in bioinformatics · Year: 2012 · PMID: 22228511 · Citations: 41

  23. Predicting protein ligand binding motions with the conformation explorer

    Flores SC, Gerstein MB

    BMC bioinformatics · Year: 2011 · PMID: 22032721 · Citations: 19

  24. Fast flexible modeling of RNA structure using internal coordinates

    Flores SC, Sherman MA, Bruns CM, Eastman P, Altman RB

    IEEE/ACM transactions on computational biology and bioinformatics · Year: 2011 · PMID: 21778523 · Citations: 81

  25. Strategies for articulated multibody-based adaptive coarse grain simulation of RNA

    Poursina M, Bhalerao KD, Flores SC, Anderson KS, Laederach A

    Methods in enzymology · Year: 2011 · PMID: 21187222 · Citations: 62

  26. Structural insights into pre-translocation ribosome motions

    Flores SC, Altman R

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · Year: 2011 · PMID: 21121048 · Citations: 9

  27. Turning limited experimental information into 3D models of RNA

    Flores SC, Altman RB

    RNA (New York, N.Y.) · Year: 2010 · PMID: 20651028 · Citations: 103

  28. Predicting RNA structure by multiple template homology modeling

    Flores SC, Wan Y, Russell R, Altman RB

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · Year: 2010 · PMID: 19908374 · Citations: 100

  29. StoneHinge: hinge prediction by network analysis of individual protein structures

    Keating KS, Flores SC, Gerstein MB, Kuhn LA

    Protein science : a publication of the Protein Society · Year: 2009 · PMID: 19180449 · Citations: 65

  30. HingeMaster: normal mode hinge prediction approach and integration of complementary predictors

    Flores SC, Keating KS, Painter J, Morcos F, Nguyen K, Merritt EA, Kuhn LA, Gerstein MB

    Proteins · Year: 2008 · PMID: 18433058 · Citations: 51

  31. [W6S8] octahedral tungsten clusters functionalized with thiophene derivatives: toward polymerizable building blocks

    Perruchas S, Flores S, Jousselme B, Lobkovsky E, Abruña H, Disalvo FJ

    Inorganic chemistry · Year: 2007 · PMID: 17883265

  32. FlexOracle: predicting flexible hinges by identification of stable domains

    Flores SC, Gerstein MB

    BMC bioinformatics · Year: 2007 · PMID: 17587456 · Citations: 54

  33. Hinge Atlas: relating protein sequence to sites of structural flexibility

    Flores SC, Lu LJ, Yang J, Carriero N, Gerstein MB

    BMC bioinformatics · Year: 2007 · PMID: 17519025 · Citations: 69

  34. Dissecting the mechanism of Epac activation via hydrogen-deuterium exchange FT-IR and structural modeling

    Yu S, Fan F, Flores SC, Mei F, Cheng X

    Biochemistry · Year: 2006 · PMID: 17176054 · Citations: 41

  35. The Database of Macromolecular Motions: new features added at the decade mark

    Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M

    Nucleic acids research · Year: 2006 · PMID: 16381870 · Citations: 185

Query: "Narrowe Danielsson S"[Author] OR "Narrowe S"[Author] | Publications: 1 | Citation matches: 1 | Scholar | ORCID

  1. Reliable Identification of Homodimers Using AlphaFold

    SN Danielsson, A Elofsson

    bioRxiv preprint · Year: 2025 · Citations: 3

Query: "Viliuga V"[Author] | Publications: 8 | Citation matches: 8 | Scholar | ORCID

  1. ABAG-Rank: improving model selection of AlphaFold antibody-antigen complexes by learning to rank

    Tadiello M, Ludaic M, Viliuga V, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2026 · PMID: 42693924 · Citations: 1

  2. Novel Insights into the Human Hsc70 Structure by Cross-Linking Mass Spectrometry and Molecular Modeling

    Melikov A, Viliuga V, Kavan D, Kukačka Z, Mayer MP, Novák P

    Journal of proteome research · Year: 2026 · PMID: 42565729 · Citations: 0

  3. Limitations of the refolding pipeline for de novo protein design

    Korbeld KT, Viliuga V, Fürst MJLJ

    Protein science : a publication of the Protein Society · Year: 2026 · PMID: 42089695 · Citations: 7

  4. Mass spectrometry integrates protein design into structural biology method development

    Stevens A, Osterholz H, Viliuga V, Vosselman T, Kokane S, Marklund EG, Elofsson A, Leppert A, Landreh M

    QRB discovery · Year: 2026 · PMID: 42063620 · Citations: 0

  5. Predicting directional flexibility in proteins

    V Viliuga, L Seute, M Tadiello, N Wolf, F Gräter, A Elofsson

    arXiv preprint · Year: 2026 · Citations: 0

  6. ColBuilder: flexible structure generation of crosslinked collagen fibrils

    Monego D, Brosz M, Buck J, Viliuga V, Greicius P, Jung J, Stuehn T, Schmies M, Sugita Y, Gräter F

    Bioinformatics (Oxford, England) · Year: 2025 · PMID: 40323309 · Citations: 6

  7. Flexibility-conditioned protein structure design with flow matching

    V Viliuga*, L Seute*, N Wolf, S Wagner, A Elofsson, J Stühmer, F Gräter

    Forty-second International Conference on Machine Learning , 2025 · Year: 2025 · Citations: 11

  8. Energy-based flow matching for generating 3D molecular structure

    W Zhou, CI Sprague, V Viliuga, M Tadiello, A Elofsson, H Azizpour

    Forty-second International Conference on Machine Learning , 2025 · Year: 2025 · Citations: 10

Query: "Ludaic M"[Author] | Publications: 3 | Citation matches: 0 | ORCID

  1. ABAG-Rank: improving model selection of AlphaFold antibody-antigen complexes by learning to rank

    Tadiello M, Ludaic M, Viliuga V, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2026 · PMID: 42693924

  2. Limits of deep-learning-based RNA prediction methods

    Ludaic M, Elofsson A

    Nucleic acids research · Year: 2026 · PMID: 42635124

  3. Evaluating deep learning based structure prediction methods on antibody-antigen complexes

    Fromm S, Ludaic M, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2026 · PMID: 41863324

Query: "Matteo Tadiello"[Author] | Publications: 2 | Citation matches: 2 | Scholar

  1. Predicting directional flexibility in proteins

    V Viliuga, L Seute, M Tadiello, N Wolf, F Gräter, A Elofsson

    arXiv preprint · Year: 2026 · Citations: 0

  2. Energy-based flow matching for generating 3D molecular structure

    W Zhou, CI Sprague, V Viliuga, M Tadiello, A Elofsson, H Azizpour

    arXiv preprint · Year: 2025 · Citations: 10

Query: "Oswal, Anu"[Author] | Publications: 1 | Citation matches: 0 | ORCID

  1. MAVISp: A modular structure-based framework for protein variant effects

    Arnaudi M, Utichi M, Degn K, Tiberti M, Beltrame L, Krzesińska K, Besora PS, Kiachaki E, Scrima S, Bauer L, Meldgård K, Melidi A, Favaro L, Oswal A, Tedeschi G, Dorčaková T, Estad AH, Breitenstein J, Safer J, Saridaki P, et al.

    Protein science : a publication of the Protein Society · Year: 2026 · PMID: 41944585

Query: "Nguyen Ngoc Vi Tran"[Author] | Publications: 0 | Citation matches: 0 | Scholar | ORCID

    Query: "Damian Sobecki"[Author] | Publications: 0 | Citation matches: 0 | Scholar | ORCID

      Query: "Ines Cunha[Author]" | Publications: 66 | Citation matches: 4 | Scholar | ORCID

      1. Epilepsy and vascular risk: Evaluation of the influence of antiseizure medications on atherosclerotic disease

        Silva C, Barros F, Faustino P, Sousa JA, Jesus-Ribeiro J, Cunha I, Martins E, Correia P, Cruto C, Coelho J, Xavier A, Jóia M, Sargento-Freitas J, Silva F, Teotónio R, Bento C, Sales F

        Epileptic disorders : international epilepsy journal with videotape · Year: 2026 · PMID: 42400469

      2. Infection-Related Adverse Drug Reactions Reported with Biologic Disease Modifying Anti-Rheumatic Drugs in Pediatric Patients: Analysis of the EudraVigilance database

        Vilafanha C, Azevedo SF, Prata AR, Cunha I, Barcelos A

        Journal of the Pediatric Infectious Diseases Society · Year: 2026 · PMID: 42286893

      3. Cognitive Dysfunction in Fibromyalgia: Prevalence and Independent Predictors-A Case-Control Study Using the Montreal Cognitive Assessment Scale

        Azevedo SF, Genrinho I, Saldanha J, Cunha I

        Brain sciences · Year: 2026 · PMID: 41594789

      4. The Medication Patterns of Spinocerebellar Ataxia Type 3 Mutation Carriers Enrolled in the ESMI Cohort

        Silva P, Costa MA, Gaspar L, Durães J, Cunha I, Ribeiro JA, Januário C, Oliveiros B, Hübener-Schmid J, Faber J, Raposo M, Lima M, Garcia-Moreno H, Giunti P, Beichert L, Schöls L, van de Warrenburg BP, de Vries J, Thieme A, Reetz K, et al.

        CNS drugs · Year: 2026 · PMID: 41105366

      5. SMLMFlow: Improving Structural Resolution in Single Molecule Localization Microscopy with Flow Matching

        S Bauer, L Panconi, I Cunha, E Latron, D Sage, R Peters, J Griffie

        bioRxiv preprint · Year: 2026 · Citations: 1

      6. Anti-Osteoporotic Medication-Related Jaw Osteonecrosis: A Descriptive Analysis of the European EudraVigilance Database

        Ferreira Azevedo S, Pinto Oliveira C, Prata AR, Cunha I, Barcelos A

        Acta medica portuguesa · Year: 2025 · PMID: 41204864

      7. Long-term outcomes of epilepsy surgery: A 25-year experience from a tertiary referral center

        Almeida M, Barros F, Cunha I, Brás A, Teotónio R, Bento C, Sales F

        Epileptic disorders : international epilepsy journal with videotape · Year: 2025 · PMID: 40913513

      8. Progression of biological markers in spinocerebellar ataxia type 3: longitudinal analysis of prospective data from the ESMI cohort

        Berger M, Garcia-Moreno H, Ferreira M, Hubener-Schmid J, Schaprian T, Wegner P, Elter T, Teichmann KM, Santana MM, Grobe-Einsler M, Oender D, Koyak BSC, Bernsen S, Pereira de Almeida L, Silva P, Ribeiro JA, Cunha I, Gonzalez-Robles C, Khan S, Heslegrave A, et al.

        The Lancet regional health. Europe · Year: 2025 · PMID: 40678042

      9. Progression of biological markers in spinocerebellar ataxia type 3: analysis of longitudinal data from the ESMI cohort

        Berger M, Garcia-Moreno H, Ferreira M, Hubener-Schmid J, Schaprian T, Wegner P, Elter T, Teichmann K, Santana MM, Grobe-Einsler M, Onder D, Koyak B, Bernsen S, de Almeida LP, Silva P, Ribeiro JA, Cunha I, Gonzalez-Robles C, Khan S, Heslegrave A, et al.

        medRxiv : the preprint server for health sciences · Year: 2025 · PMID: 39974031

      10. Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework

        Saraiva BM, Cunha I, Brito AD, Follain G, Portela R, Haase R, Pereira PM, Jacquemet G, Henriques R

        Nature methods · Year: 2025 · PMID: 39747509 · Citations: 26

      11. AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI

        I Cunha, L Panconi, S Bauer, M Gestin, E Latron, E Sahai, A Le Marois, ...

        bioRxiv preprint · Year: 2025 · Citations: 2

      12. Machine learning in microscopy - insights, opportunities and challenges

        Cunha I, Latron E, Bauer S, Sage D, Griffié J

        Journal of cell science · Year: 2024 · PMID: 39465533 · Citations: 27

      13. Safety of direct oral provocation test to delabel reported mild beta-lactam allergy in infants

        Cunha F, Cunha I, Gomes E

        Allergologia et immunopathologia · Year: 2024 · PMID: 38459885

      14. Colouterine Fistula as a Rare Cause of Postmenopausal Abnormal Uterine Bleeding: A Case Report

        Silva C, Monteiro C, Barbosa F, Cunha I, Coutada R, Carvalho A

        Journal of clinical medicine · Year: 2024 · PMID: 38337477

      15. Correction to: The frequency of non‑motor symptoms in SCA3 and their association with disease severity and lifestyle factors

        Hengel H, Martus P, Faber J, Giunti P, Garcia-Moreno H, Solanky N, Klockgether T, Reetz K, van de Warrenburg BP, Santana MM, Silva P, Cunha I, de Almeida LP, Timmann D, Infante J, de Vries J, Lima M, Pires P, Bushara K, Jacobi H, et al.

        Journal of neurology · Year: 2024 · PMID: 37979094

      16. Influence of the timing of biological treatment initiation on Juvenile Idiopathic Arthritis long-term outcomes

        Oliveira Ramos F, Rodrigues AM, Melo AT, Aguiar F, Brites L, Azevedo S, Duarte AC, Gomes JAM, Furtado C, Mourão AF, Sequeira G, Cunha I, Figueira R, Santos MJ, Fonseca JE

        Arthritis research & therapy · Year: 2023 · PMID: 37735435

      17. Effectiveness of biosimilar infliximab CT-P13 compared to originator infliximab in biological-naïve patients with rheumatoid arthritis and axial spondyloarthritis: data from the Portuguese Register

        Marona J, Sepriano A, Ramiro S, Almeida D, Brites L, Couto M, Cunha I, Fernandes BM, Garcia J, Melo AT, Nóvoa T, Oliveira M, Pinto P, Santos MJ, Silva C, Fonseca JE, Araújo FC

        ARP rheumatology · Year: 2023 · PMID: 37421191

      18. Phenytoin-Induced Toxic Epidermal Necrolysis in a Pediatric Patient

        Pinto AR, Cunha IM, Gomes ER

        The journal of allergy and clinical immunology. In practice · Year: 2023 · PMID: 36878750

      19. A standardised protocol for blood and cerebrospinal fluid collection and processing for biomarker research in ataxia

        Santana MM, Gaspar LS, Pinto MM, Silva P, Adão D, Pereira D, Ribeiro JA, Cunha I, Huebener-Schmid J, Raposo M, Ferreira AF, Faber J, Kuhs S, Garcia-Moreno H, Reetz K, Thieme A, Infante J, van de Warrenburg BPC, Giunti P, Riess O, et al.

        Neuropathology and applied neurobiology · Year: 2023 · PMID: 36798010

      20. Impact of the COVID-19 Pandemic on the Prescribing of Antiasthmatic Treatments in Portugal: A Nationwide Study

        Silva TM, Pinto BS, Cunha I, Roque F, Figueiras A, Fonseca J, Herdeiro MT, Gomes ER

        Clinical therapeutics · Year: 2023 · PMID: 36775690

      21. Food Allergy to Sheep's Milk Proteins with Cow's Milk Tolerance in an Adult Patient

        Cunha IM, Pinto AR, Bartolomé B, Falcão H

        Acta medica portuguesa · Year: 2023 · PMID: 36592483

      22. The frequency of non-motor symptoms in SCA3 and their association with disease severity and lifestyle factors

        Hengel H, Martus P, Faber J, Giunit P, Garcia-Moreno H, Solanky N, Klockgether T, Reetz K, van de Warrenburg BP, Santana MM, Silva P, Cunha I, de Almeida LP, Timmann D, Infante J, de Vries J, Lima M, Pires P, Bushara K, Jacobi H, et al.

        Journal of neurology · Year: 2023 · PMID: 36324033

      23. Carbon-Yarn-Based Supercapacitors with In Situ Regenerated Cellulose Hydrogel for Sustainable Wearable Electronics

        Carvalho JT, Cunha I, Coelho J, Fortunato E, Martins R, Pereira L

        ACS applied energy materials · Year: 2022 · PMID: 36311466

      24. Reply to Comment on "Patients' Postjudice of Tele-Neurology for Movement Disorders"

        Rajapakshe I, Menozzi E, Cunha I, Lees AJ, Bhatia KP, Mulroy E

        Movement disorders clinical practice · Year: 2022 · PMID: 36247909

      25. Systemic autoinflammatory diseases in pediatric population

        Marques ML, Cunha IM, Alves S, Guedes M, Zilhão C

        Asia Pacific allergy · Year: 2022 · PMID: 35966154

      26. Spastic Paraplegia Type 7 and Movement Disorders: Beyond the Spastic Paraplegia

        Sáenz-Farret M, Lang AE, Kalia L, Cunha I, Sousa M, Kuhlman G, Ganos C, Munhoz RP, Fasano A, Piña-Avilés CE, Zúñiga-Ramírez C

        Movement disorders clinical practice · Year: 2022 · PMID: 35586535

      27. Patients' Postjudice of Tele-Neurology for Movement Disorders

        Rajapakshe I, Menozzi E, Cunha I, Lees AJ, Bhatia KP, Mulroy E

        Movement disorders clinical practice · Year: 2022 · PMID: 35586530

      28. Association between self-reported drug hypersensitivity reactions and psychological disorders

        Cunha IM, Gouveia J, Gomes E

        Asia Pacific allergy · Year: 2022 · PMID: 35571546

      29. Treatment-Resistant Depression in Portugal: Perspective From Psychiatry Experts

        Bessa JM, Carvalho S, Cunha IB, Fernandes M, Matos-Pires A, Neves R, Oliveira-Maia AJ, Santos S, Santos V

        Frontiers in psychiatry · Year: 2022 · PMID: 35432028

      30. Dupilumab: A Safe and Successful Treatment in Refractory Prurigo Nodularis

        Cunha IM, Valadão I, Gomes E, Marinho A

        The journal of allergy and clinical immunology. In practice · Year: 2022 · PMID: 35331683

      31. Hereditary spastic paraparesis: The real-world experience from a Neurogenetics outpatient clinic

        Cunha IA, Ribeiro JA, Santos MC

        European journal of medical genetics · Year: 2022 · PMID: 35065294

      32. An Atypical Presentation of a Colonic Lipoma: Avoiding Surgery with a Deeper Endoscopic Look

        João M, Cunha I, Gravito-Soares E, Gravito-Soares M, Amaro P, Figueiredo P

        GE Portuguese journal of gastroenterology · Year: 2021 · PMID: 35111963

      33. Health-related quality of life and disability in adults with juvenile idiopathic arthritis: comparison with adult-onset rheumatic diseases

        Oliveira Ramos F, Rodrigues A, Magalhaes Martins F, Melo AT, Aguiar F, Brites L, Azevedo S, Duarte AC, Furtado C, Mourão AF, Sequeira G, Cunha I, Figueira R, Melo Gomes JA, Santos MJ, Fonseca JE

        RMD open · Year: 2021 · PMID: 34819385

      34. Reusable and highly sensitive SERS immunoassay utilizing gold nanostars and a cellulose hydrogel-based platform

        Oliveira MJ, Cunha I, de Almeida MP, Calmeiro T, Fortunato E, Martins R, Pereira L, Byrne HJ, Pereira E, Águas H, Franco R

        Journal of materials chemistry. B · Year: 2021 · PMID: 34551048

      35. Ionic Conductive Cellulose Mats by Solution Blow Spinning as Substrate and a Dielectric Interstrate Layer for Flexible Electronics

        Claro PIC, Cunha I, Paschoalin RT, Gaspar D, Miranda K, Oliveira ON Jr, Martins R, Pereira L, Marconcini JM, Fortunato E, Mattoso LHC

        ACS applied materials & interfaces · Year: 2021 · PMID: 34038087

      36. Recurrent neck swelling after iodinated contrast media administration

        Cunha IM, Maganinho P, Marques ML, Amorim JP, Gomes E

        Radiology case reports · Year: 2021 · PMID: 33981373

      37. Vitamin D deficiency in a Portuguese epilepsy cohort: who is at risk and how to treat

        Cunha IA, Saraiva AM, Lopes P, Jesus-Ribeiro J, Duarte C, Leitão F, Sales F, Santana I, Bento C

        Epileptic disorders : international epilepsy journal with videotape · Year: 2021 · PMID: 33875410

      38. Sporadic Creutzfeldt-Jakob disease presenting as epilepsia partialis continua and non-ictal nystagmus

        Cunha IA, Gomes I, Gens H, Guimarães S, Martins AI, Bento C

        European journal of neurology · Year: 2021 · PMID: 33786955

      39. Static and Dynamic Ocular Motor Abnormalities as Potential Biomarkers in Spinocerebellar Ataxia Type 3

        Lemos J, Novo A, Duque C, Cunha I, Ribeiro J, Castelhano J, Januário C

        Cerebellum (London, England) · Year: 2021 · PMID: 33215370

      40. Endoscopic Management of Gastric Penetration by a Fishbone

        Cunha I, Barreto L, Perdigoto DN, Figueiredo P

        GE Portuguese journal of gastroenterology · Year: 2020 · PMID: 33564708

      41. Remission and low disease activity matrix tools: results in real-world rheumatoid arthritis patients under anti-TNF therapy

        Ganhão S, Lucas R, Fonseca JE, Santos MJ, Gonçalves DR, Madeira N, Silva C, Dourado E, Freitas R, Rodrigues J, Azevedo S, Rocha TM, Ferreira RM, Garcia S, Fernandes BM, Prata AR, Couto M, Torres RP, Cunha I, Costa L, et al.

        Acta reumatologica portuguesa · Year: 2020 · PMID: 33420771

      42. Anaphylaxis to Agaricus bisporus ingestion

        Cunha IM, Marques ML, Abreu C, Bartolomé B, Gomes E

        Einstein (Sao Paulo, Brazil) · Year: 2020 · PMID: 33263677

      43. Dieulafoy Lesion: Predictive Factors of Early Relapse and Long-Term Follow-Up

        Massinha P, Cunha I, Tomé L

        GE Portuguese journal of gastroenterology · Year: 2020 · PMID: 32775545

      44. The role of opioid analgesics in rheumatic disorders: a position paper from the Portuguese Rheumatology Society

        Azevedo S, Guimarães F, Leite Silva J, Barros R, Capela S, Abreu P, Cunha Miranda L, Dourado E, Faustino A, Ferreira J, Las V, Martins F, Martins Rocha T, Meirinhos T, Salvador MJ, Santos-Faria D, Soares Rodrigues M, Teixeira F, Cunha I

        Acta reumatologica portuguesa · Year: 2020 · PMID: 32572015

      45. Pancreas- and Pylorus-Preserving Duodenectomy for Advanced Familial Duodenal Polyposis

        Leite JS, Tralhão JG, Manso A, Fernandes M, Cunha I, Amaro P

        GE Portuguese journal of gastroenterology · Year: 2020 · PMID: 32509924

      46. Prevalence, risk factors and global impact of musculoskeletal injuries among endoscopists: a nationwide European study

        Morais R, Vilas-Boas F, Pereira P, Lopes P, Simões C, Dantas E, Cunha I, Roseira J, Cortez-Pinto J, Silva J, Lage J, Caine M, Rocha M, Flor de Lima M, Costa Santos MP, Garrido M, Sousa P, Marcos P, Azevedo R, Castro R, et al.

        Endoscopy international open · Year: 2020 · PMID: 32258368

      47. The impact of demographic and clinical characteristics on diabetic painful neuropathy

        Assunção A, Campos D, Marques R, Cunha I, Santos P, Martins A, Gonçalves AS, Rebelo A, Lima C, Matos C, Prata AC, Teixeira JT, Duarte L, Belo M, Figueiredo P, Rosa TL

        Romanian journal of internal medicine = Revue roumaine de medecine interne · Year: 2020 · PMID: 31446430

      48. 12-Year-old Female with Mucocutaneous Lesions

        Marujo F, Conde M, Ferreira C, Cunha I, Gouveia C

        The Pediatric infectious disease journal · Year: 2019 · PMID: 31626051

      49. Endoscopic Resection of a Rectal Neuroendocrine Tumor: Hybrid Endoscopic Submucosal Dissection

        Gravito-Soares M, Gravito-Soares E, Amaro P, Cunha I, Fraga J, Tomé L

        GE Portuguese journal of gastroenterology · Year: 2019 · PMID: 30976620

      50. Fully Printed Zinc Oxide Electrolyte-Gated Transistors on Paper

        Carvalho JT, Dubceac V, Grey P, Cunha I, Fortunato E, Martins R, Clausner A, Zschech E, Pereira L

        Nanomaterials (Basel, Switzerland) · Year: 2019 · PMID: 30704027

      51. Clinical Practice Impact of the Boston Bowel Preparation Scale in a European Country

        Massinha P, Almeida N, Cunha I, Tomé L

        GE Portuguese journal of gastroenterology · Year: 2018 · PMID: 30320161

      52. Uncertainties in the Management of a Lynch Syndrome Patient: A Case Report

        Campos S, Amaro P, Cunha I, Fraga J, Cipriano MA, Tomé L

        GE Portuguese journal of gastroenterology · Year: 2017 · PMID: 29255760

      53. Shoulder giant schwannoma - a diagnosis to be considered in painless shoulder masses

        Pinho R, Santana S, Farinha F, Cunha I, Barcelos A, Brenha J

        Acta reumatologica portuguesa · Year: 2017 · PMID: 29132141

      54. Portuguese recommendations for the use of biological therapies in patients with axial spondyloarthritis - 2016 update

        Machado P, Cerqueira M, Ávila-Ribeiro P, Aguiar R, Bernardo A, Sepriano A, Águeda A, Cordeiro A, Raposo A, Rodrigues AM, Barcelos A, Malcata A, Lopes C, Vaz CC, Nour D, Godinho F, Alvarenga F, Pimentel-Santos F, Canhão H, Santos H, et al.

        Acta reumatologica portuguesa · Year: 2017 · PMID: 28894079

      55. Concerns of patients with systemic lupus erythematosus and adherence to therapy - a qualitative study

        Farinha F, Freitas F, Águeda A, Cunha I, Barcelos A

        Patient preference and adherence · Year: 2017 · PMID: 28761334

      56. [Predictors of changes in functional capacity on a cardiac rehabilitation program]

        Branco CF, Viamonte S, Matos C, Magalhães S, Cunha I, Barreira A, Fernandes P, Torres S

        Revista portuguesa de cardiologia : orgao oficial da Sociedade Portuguesa de Cardiologia = Portuguese journal of cardiology : an official journal of the Portuguese Society of Cardiology · Year: 2016 · PMID: 27006062

      57. Utilization of Subcutaneous Methotrexate in Rheumatoid Arthritis Patients After Failure or Intolerance to Oral Methotrexate: A Multicenter Cohort Study

        Branco JC, Barcelos A, de Araújo FP, Sequeira G, Cunha I, Patto JV, Oliveira M, Mateus MP, Couto M, Nero P, Pinto P, Monteiro P, Castelão W, Félix J, Ferreira D, Almeida J, Silva MJ

        Advances in therapy · Year: 2016 · PMID: 26724937

      58. DAS28, CDAI and SDAI cut-offs do not translate the same information: results from the Rheumatic Diseases Portuguese Register Reuma.pt

        Martins FM, da Silva JA, Santos MJ, Vieira-Sousa E, Duarte C, Santos H, Costa JA, Pimentel-Santos FM, Cunha I, Cunha Miranda L, Nóvoa T, Cruz M, Bernardes M, Araujo D, Pereira Silva JA, Silva JC, Branco JC, Gomes JA, Faustino A, Fonseca JE, et al.

        Rheumatology (Oxford, England) · Year: 2015 · PMID: 25173347

      59. The Portuguese Society of Rheumatology position paper on the use of biosimilars

        Fonseca JE, Gonçalves J, Araújo F, Cordeiro I, Teixeira F, Canhão H, da Silva JA, Garcês S, Miranda LC, Ramiro S, Roxo A, Pimentel-Santos FM, Tavares V, Neto A, Sepriano A, Malcata A, Faustino A, Silva C, Ambrósio C, Duarte C, et al.

        Acta reumatologica portuguesa · Year: 2014 · PMID: 24811463

      60. Newest Vital Sign as a proxy for medication adherence in older adults

        Salgado TM, Ramos SB, Sobreira C, Canas R, Cunha I, Benrimoj SI, Fernandez-Llimos F

        Journal of the American Pharmacists Association : JAPhA · Year: 2013 · PMID: 24091561

      61. Portuguese recommendations for the use of biological therapies in patients with axial spondyloarthritis--December 2011 update

        Machado P, Bernardo A, Cravo AR, Rodrigues A, Malcata A, Nour D, Vieira-Sousa E, Godinho F, Pimentel F, Canhão H, Santos H, Cunha I, Fonseca JE, Costa J, Costa L, Cunha-Miranda L, Maurício L, Cruz M, Santos MJ, Bernardes M, et al.

        Acta reumatologica portuguesa · Year: 2012 · PMID: 22781513

      62. Portuguese guidelines for the use of biological agents in rheumatoid arthritis - October 2011 update

        Fonseca JE, Bernardes M, Canhão H, Santos MJ, Quintal A, Malcata A, Neto A, Cordeiro A, Rodrigues A, Mourão AF, Ribeiro AS, Cravo AR, Barcelos A, Cardoso A, Vilar A, Braña A, Faustino A, Silva C, Duarte C, Araújo D, et al.

        Acta reumatologica portuguesa · Year: 2011 · PMID: 22472929

      63. Portuguese guidelines for the use of biological agents in rheumatoid arthritis - March 2010 update

        Fonseca JE, Canhão H, Reis P, Santos MJ, Branco J, Quintal A, Malcata A, Araújo D, Ventura F, Figueiredo G, da Silva JC, Patto JV, de Queiroz MV, Santos RA, Neto AJ, de Matos Ad, Rodrigues A, Mourão AF, Ribeiro AS, Cravo AR, et al.

        Acta reumatologica portuguesa · Year: 2010 · PMID: 20505635

      64. Quality of life after surgery for temporal lobe epilepsy: a 5-year follow-up

        Cunha I, Oliveira J

        Epilepsy & behavior : E&B · Year: 2010 · PMID: 20199891

      65. [Cyclophosphamide induced amenorrhoea in pre-menopausal women with systemic lupus erythematosus]

        Cunha I, Saavedra MJ, Pereira da Silva JA, Malcata A

        Acta reumatologica portuguesa · Year: 2008 · PMID: 18344924

      66. Comparison between the results of the Symptom Checklist-90 in two different populations with temporal lobe epilepsy

        Cunha I, Brissos S, Dinis M, Mendes I, Nobre A, Passão V

        Epilepsy & behavior : E&B · Year: 2003 · PMID: 14698709

      Query: "Goldtzvik, Y"[Author] | Publications: 9 | Citation matches: 9 | Scholar | ORCID

      1. AlphaFold Database expands to proteome-scale quaternary structures

        Y Han, MI Tsenkov, NAE Venanzi, S Cha, N Patel, S Nair, R Abbara, ...

        bioRxiv preprint · Year: 2026 · Citations: 13

      2. Lever Arm Flexibility Controls the Extent of (Un)Coupling to the Motor Domain in Myosin Motors

        Mugnai ML, Goldtzvik Y, Thirumalai D

        The journal of physical chemistry. B · Year: 2025 · PMID: 41037333 · Citations: 0

      3. Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

        Waman VP, Ashford P, Lam SD, Sen N, Abbasian M, Woodridge L, Goldtzvik Y, Bordin N, Wu J, Sillitoe I, Orengo CA

        Scientific reports · Year: 2024 · PMID: 38902252 · Citations: 4

      4. Protein diversification through post-translational modifications, alternative splicing, and gene duplication

        Goldtzvik Y, Sen N, Lam SD, Orengo C

        Current opinion in structural biology · Year: 2023 · PMID: 37354790 · Citations: 61

      5. Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application to Kinesin

        Goldtzvik Y, Thirumalai D

        Journal of chemical theory and computation · Year: 2021 · PMID: 34251798 · Citations: 4

      6. How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics

        Takaki R, Mugnai ML, Goldtzvik Y, Thirumalai D

        Proceedings of the National Academy of Sciences of the United States of America · Year: 2019 · PMID: 31659052 · Citations: 20

      7. Dynamics of Allosteric Transitions in Dynein

        Goldtzvik Y, Mugnai ML, Thirumalai D

        Structure (London, England : 1993) · Year: 2018 · PMID: 30270176 · Citations: 23

      8. Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin

        Zhang Z, Goldtzvik Y, Thirumalai D

        Proceedings of the National Academy of Sciences of the United States of America · Year: 2017 · PMID: 29087307 · Citations: 37

      9. Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin

        Goldtzvik Y, Zhang Z, Thirumalai D

        The journal of physical chemistry. B · Year: 2016 · PMID: 26702870 · Citations: 22

      Query: "Deeksha Thakur"[Author] | Publications: 2 | Citation matches: 2 | Scholar | ORCID

      1. Uncovering the translatome impact of transcriptome induced diversity in eukaryotes: framework and innovative insights

        P Verma, D Thakur, SB Pandit

        bioRxiv preprint · Year: 2024 · Citations: 0

      2. Exon Nomenclature and Classification of Transcripts (ENACT): Systematic framework to annotate exon attributes

        P Verma, D Thakur, SB Pandit

        bioRxiv preprint · Year: 2024 · Citations: 0

      Query: "Saurov Hazarika"[Author] | Publications: 0 | Citation matches: 0 | Scholar | ORCID

        Query: "Panconi L"[Author] | Publications: 9 | Citation matches: 9 | Scholar | ORCID

        1. Nanoscale protein clustering modulates the input-output response of cellular signalling pathways

          Panconi L, Griffié J, Owen DM

          Scientific reports · Year: 2026 · PMID: 42581073 · Citations: 0

        2. SMLMFlow: Improving Structural Resolution in Single Molecule Localization Microscopy with Flow Matching

          S Bauer, L Panconi, I Cunha, E Latron, D Sage, R Peters, J Griffie

          bioRxiv preprint · Year: 2026 · Citations: 1

        3. Direct visualization of Na, K-ATPase clustering by 3D DNA-PAINT MINFLUX nanoscopy

          B Stojcic, A Agostinho, L Panconi, H Blom, H Brismar

          bioRxiv preprint · Year: 2026 · Citations: 0

        4. AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI

          I Cunha, L Panconi, S Bauer, M Gestin, E Latron, E Sahai, A Le Marois, ...

          bioRxiv preprint · Year: 2025 · Citations: 2

        5. Mapping membrane biophysical nano-environments

          Panconi L, Euchner J, Tashev SA, Makarova M, Herten DP, Owen DM, Nieves DJ

          Nature communications · Year: 2024 · PMID: 39511199 · Citations: 21

        6. Three-dimensional topology-based analysis segments volumetric and spatiotemporal fluorescence microscopy

          Panconi L, Tansell A, Collins AJ, Makarova M, Owen DM

          Biological imaging · Year: 2023 · PMID: 38516632 · Citations: 5

        7. Cluster analysis for localisation-based data sets: dos and don'ts when quantifying protein aggregates

          Panconi L, Owen DM, Griffié J

          Frontiers in bioinformatics · Year: 2023 · PMID: 38076028 · Citations: 5

        8. Phospholipid tail asymmetry allows cellular adaptation to anoxic environments

          Panconi L, Lorenz CD, May RC, Owen DM, Makarova M

          The Journal of biological chemistry · Year: 2023 · PMID: 37562570 · Citations: 16

        9. Topology-based fluorescence image analysis for automated cell identification and segmentation

          Panconi L, Makarova M, Lambert ER, May RC, Owen DM

          Journal of biophotonics · Year: 2023 · PMID: 36349740 · Citations: 9

        Query: "Cucchi, Ivan"[Author] | Publications: 3 | Citation matches: 3 | Scholar | ORCID

        1. MOLECULE: Molecular-dynamics and Optimized deep Learning for Entropy-regularized Classification and Uncertainty-aware Ligand Evaluation

          Cucchi I, Frasnetti E, Frigerio F, Cinquini F, Pavoni S, Pavarino LF, Colombo G

          Journal of chemical theory and computation · Year: 2025 · PMID: 40931675 · Citations: 3

        2. Large-scale energy decomposition for the analysis of protein stability

          Mansoor S, Frasnetti E, Cucchi I, Magni A, Bonollo G, Serapian SA, Pavarino LF, Colombo G

          Cell stress & chaperones · Year: 2025 · PMID: 39884551 · Citations: 3

        3. Integrating Molecular Dynamics and Machine Learning Algorithms to Predict the Functional Profile of Kinase Ligands

          Frasnetti E, Cucchi I, Pavoni S, Frigerio F, Cinquini F, Serapian SA, Pavarino LF, Colombo G

          Journal of chemical theory and computation · Year: 2024 · PMID: 39387368 · Citations: 19