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Publications

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

Updated
2026-04-28T18:45:34Z
PI Publications
197
PI Citation Matches
194
PI Scholar
26155 citations · h-index 80
Group Unique Papers
323
Group Unique Citations
29566
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. 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: 8 · Source: pubmed

  2. 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: 0 · Source: pubmed

  3. 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: 3 · Source: pubmed

  4. AlphaFold3 at CASP16

    Elofsson A

    Proteins · Year: 2026 · PMID: 40851426 · Citations: 22 · Source: pubmed

  5. Engaging the Community: CASP Special Interest Groups

    Elofsson A, Kretsch RC, Magnus M, Montelione GT

    Proteins · Year: 2026 · PMID: 40304050 · Citations: 4 · Source: pubmed

  6. ABAG-Rank: Improving Model Selection of AlphaFold Antibody-Antigen Complexes by Learning to Rank

    M Tadiello, M Ludaic, V Viliuga, A Elofsson

    bioRxiv preprint · Year: 2026 · Citations: 0 · Source: biorxiv

  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.

    bioRxiv : the preprint server for biology · Year: 2025 · PMID: 41279659 · Citations: 3 · Source: pubmed

  8. 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: 9 · Source: pubmed

  9. Editorial overview: Sequences and topology (2025)

    Elofsson A, Kolodny R

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

  10. Unlocking protein networks with Predictomes: The SPOC advantage

    Elofsson A

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

  11. 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: 9 · Source: pubmed

  12. 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: 2 · Source: pubmed

  13. Reliable Identification of Homodimers Using AlphaFold

    SN Danielsson, A Elofsson

    bioRxiv preprint · Year: 2025 · Citations: 1 · Source: biorxiv

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

    M Ludaic, A Elofsson

    bioRxiv preprint · Year: 2025 · Citations: 5 · Source: biorxiv

  15. 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: 6 · Source: arxiv

  16. 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: 4 · Source: arxiv

  17. 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: 13 · Source: pubmed

  18. 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: 34 · Source: pubmed

  19. 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: 30 · Source: pubmed

  20. Stable Autonomous Flow Matching

    Christopher Iliffe Sprague, Arne Elofsson, Hossein Azizpour

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

  21. 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

  22. Incorporating stability into flow matching

    CI Sprague, A Elofsson, H Azizpour

    ICML 2024 Workshop on Structured Probabilistic Inference {\&} Generative … , 2024 · Year: 2024 · Citations: 3 · Source: conference

  23. Hessian-Informed Flow Matching

    Christopher Iliffe Sprague, Arne Elofsson, Hossein Azizpour

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

  24. 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: 3 · Source: arxiv

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

    Bryant P, Elofsson A

    Communications chemistry · Year: 2023 · PMID: 37880344 · Citations: 39 · Source: pubmed

  26. 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: 13 · Source: pubmed

  27. 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: 47 · Source: pubmed

  28. 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: 197 · Source: pubmed

  29. 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: 23 · Source: pubmed

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

    Elofsson A

    Current opinion in structural biology · Year: 2023 · PMID: 37060758 · Citations: 119 · Source: pubmed

  31. 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: 9 · Source: pubmed

  32. 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: 20 · Source: pubmed

  33. 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: 38 · Source: pubmed

  34. 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

  35. 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: 725 · Source: pubmed

  36. 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

  37. 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

  38. 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: 22 · Source: pubmed

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

    Bryant P, Pozzati G, Elofsson A

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

  40. Improved prediction of protein-protein interactions using AlphaFold2

    Bryant P, Pozzati G, Elofsson A

    Nature communications · Year: 2022 · PMID: 35273146 · Citations: 1181 · Source: pubmed

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

    Pozzati G, Kundrotas P, Elofsson A

    Proteins · Year: 2022 · PMID: 35246997 · Citations: 8 · Source: pubmed

  42. 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

  43. 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: 16 · Source: pubmed

  44. 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: 185 · Source: pubmed

  45. 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

  46. Toward Characterising the Cellular 3D-Proteome

    Elofsson A

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

  47. 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: 47 · Source: pubmed

  48. 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

  49. 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: 8 · Source: pubmed

  50. 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

  51. 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

  52. 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: 156 · Source: pubmed

  53. 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: 75 · Source: pubmed

  54. 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: 4 · Source: pubmed

  55. 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: 16 · Source: pubmed

  56. 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: 2 · Source: pubmed

  57. 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: 47 · Source: pubmed

  58. 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: 66 · Source: pubmed

  59. 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: 290 · Source: pubmed

  60. 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

  61. 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: 1122 · Source: pubmed

  62. 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: 12 · Source: pubmed

  63. 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: 122 · Source: pubmed

  64. 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: 107 · Source: pubmed

  65. 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

  66. 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

  67. 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: 44 · Source: pubmed

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

    Michel M, Menéndez Hurtado D, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2019 · PMID: 30590407 · Citations: 108 · Source: pubmed

  69. 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

  70. 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: 43 · Source: pubmed

  71. 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

  72. 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: 18 · Source: pubmed

  73. 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: 37 · Source: pubmed

  74. 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

  75. 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

  76. 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: 84 · Source: pubmed

  77. 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: 17 · Source: pubmed

  78. 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: 205 · Source: pubmed

  79. 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

  80. 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: 354 · Source: pubmed

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

    Uziela K, Shu N, Wallner B, Elofsson A

    Scientific reports · Year: 2016 · PMID: 27698390 · Citations: 126 · Source: pubmed

  82. 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: 98 · Source: pubmed

  83. 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: 94 · Source: pubmed

  84. 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: 66 · Source: pubmed

  85. 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: 277 · Source: pubmed

  86. 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: 59 · Source: pubmed

  87. 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: 1053 · Source: pubmed

  88. 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: 77 · Source: pubmed

  89. 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: 67 · Source: pubmed

  90. 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: 190 · Source: pubmed

  91. 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: 115 · Source: pubmed

  92. 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: 37 · Source: pubmed

  93. 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: 19 · Source: pubmed

  94. 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

  95. 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

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

    Peters C, Elofsson A

    Proteins · Year: 2014 · PMID: 24753217 · Citations: 31 · Source: pubmed

  97. 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: 99 · Source: pubmed

  98. 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

  99. 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: 100 · Source: pubmed

  100. 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

  101. 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

  102. 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: 42 · Source: pubmed

  103. Ligand binding properties of human galanin receptors

    Jurkowski W, Yazdi S, Elofsson A

    Molecular membrane biology · Year: 2013 · PMID: 23237663 · Citations: 26 · Source: pubmed

  104. 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: 42 · Source: pubmed

  105. 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

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

    Hayat S, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2012 · PMID: 22689784 · Citations: 14 · Source: pubmed

  107. 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

  108. 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: 261 · Source: pubmed

  109. 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: 30 · Source: pubmed

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

    Hayat S, Elofsson A

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

  111. 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: 437 · Source: pubmed

  112. 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: 44 · Source: pubmed

  113. An introduction to membrane proteins

    Hedin LE, Illergård K, Elofsson A

    Journal of proteome research · Year: 2011 · PMID: 21815691 · Citations: 148 · Source: pubmed

  114. 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

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

    Shu N, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2011 · PMID: 21505030 · Citations: 9 · Source: pubmed

  116. Rapid membrane protein topology prediction

    Hennerdal A, Elofsson A

    Bioinformatics (Oxford, England) · Year: 2011 · PMID: 21493661 · Citations: 67 · Source: pubmed

  117. 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

  118. 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

  119. 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: 40 · Source: pubmed

  120. 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

  121. 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: 20 · Source: pubmed

  122. 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

  123. 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

  124. 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: 88 · Source: pubmed

  125. Identifying and quantifying orphan protein sequences in fungi

    Ekman D, Elofsson A

    Journal of molecular biology · Year: 2010 · PMID: 19944701 · Citations: 80 · Source: pubmed

  126. 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: 129 · Source: pubmed

  127. 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: 83 · Source: pubmed

  128. 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: 704 · Source: pubmed

  129. TOPCONS: consensus prediction of membrane protein topology

    Bernsel A, Viklund H, Hennerdal A, Elofsson A

    Nucleic acids research · Year: 2009 · PMID: 19429891 · Citations: 643 · Source: pubmed

  130. 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: 286 · Source: pubmed

  131. 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: 30 · Source: pubmed

  132. 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: 274 · Source: pubmed

  133. 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

  134. 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: 366 · Source: pubmed

  135. 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: 482 · Source: pubmed

  136. 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: 212 · Source: pubmed

  137. 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

  138. 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

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

    Wallner B, Elofsson A

    Proteins · Year: 2007 · PMID: 17894353 · Citations: 121 · Source: pubmed

  140. 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

  141. Pcons.net: protein structure prediction meta server

    Wallner B, Larsson P, Elofsson A

    Nucleic acids research · Year: 2007 · PMID: 17584798 · Citations: 78 · Source: pubmed

  142. Membrane protein structure: prediction versus reality

    Elofsson A, von Heijne G

    Annual review of biochemistry · Year: 2007 · PMID: 17579561 · Citations: 329 · Source: pubmed

  143. 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: 53 · Source: pubmed

  144. Expansion of protein domain repeats

    Björklund AK, Ekman D, Elofsson A

    PLoS computational biology · Year: 2006 · PMID: 16933986 · Citations: 306 · Source: pubmed

  145. 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: 65 · Source: pubmed

  146. 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

  147. 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: 115 · Source: pubmed

  148. 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: 49 · Source: pubmed

  149. 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: 457 · Source: pubmed

  150. 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: 239 · Source: pubmed

  151. Preferential attachment in the evolution of metabolic networks

    Light S, Kraulis P, Elofsson A

    BMC genomics · Year: 2005 · PMID: 16281983 · Citations: 99 · Source: pubmed

  152. 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

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

    Wallner B, Elofsson A

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

  154. 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: 243 · Source: pubmed

  155. Tertiary windowing to detect positive diversifying selection

    Berglund AC, Wallner B, Elofsson A, Liberles DA

    Journal of molecular evolution · Year: 2005 · PMID: 15883884 · Citations: 46 · Source: pubmed

  156. 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: 299 · Source: pubmed

  157. 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: 301 · Source: pubmed

  158. 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

  159. 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

  160. 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: 318 · Source: pubmed

  161. 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

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

    Rychlewski L, Fischer D, Elofsson A

    Proteins · Year: 2003 · PMID: 14579344 · Citations: 87 · Source: pubmed

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

    Wallner B, Fang H, Elofsson A

    Proteins · Year: 2003 · PMID: 14579343 · Citations: 155 · Source: pubmed

  164. 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: 153 · Source: pubmed

  165. 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: 128 · Source: pubmed

  166. 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: 921 · Source: pubmed

  167. Can correct protein models be identified?

    Wallner B, Elofsson A

    Protein science : a publication of the Protein Society · Year: 2003 · PMID: 12717029 · Citations: 867 · Source: pubmed

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

    Dönnes P, Elofsson A

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

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

    Milchert LE, Liberles DA, Elofsson A

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

  170. 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

  171. A study on protein sequence alignment quality

    Elofsson A

    Proteins · Year: 2002 · PMID: 11835508 · Citations: 96 · Source: pubmed

  172. 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: 101 · Source: pubmed

  173. 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: 136 · Source: pubmed

  174. 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: 386 · Source: pubmed

  175. 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: 281 · Source: pubmed

  176. Structure prediction meta server

    Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

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

  177. 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: 142 · Source: pubmed

  178. 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

  179. 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: 491 · Source: pubmed

  180. 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

  181. Study of the electrostatics treatment in molecular dynamics simulations

    Garemyr R, Elofsson A

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

  182. 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: 117 · Source: pubmed

  183. 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

  184. 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

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

    Hargbo J, Elofsson A

    Proteins · Year: 1999 · PMID: 10373007 · Citations: 113 · Source: pubmed

  186. 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

  187. 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: 67 · Source: pubmed

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

    Mingarro I, Elofsson A, von Heijne G

    Journal of molecular biology · Year: 1997 · PMID: 9325117 · Citations: 46 · Source: pubmed

  189. 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: 1386 · Source: pubmed

  190. 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: 193 · Source: pubmed

  191. 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: 191 · Source: pubmed

  192. 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: 72 · Source: pubmed

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

    Elofsson A, Le Grand SM, Eisenberg D

    Proteins · Year: 1995 · PMID: 8539252 · Citations: 87 · Source: pubmed

  194. 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

  195. 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

  196. 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

  197. 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: 74 | Citation matches: 73 | Scholar | ORCID

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

    Collins KW, Copeland MM, Kundrotas PJ, Vakser IA

    Journal of molecular biology · Year: 2025 · PMID: 41274550 · Citations: 0

  2. 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

  3. 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: 5

  4. 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: 3

  5. 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: 5

  6. 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: 38

  7. 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: 14

  8. 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: 125

  9. 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: 197

  10. Editorial: Protein recognition and associated diseases

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

    Frontiers in bioinformatics · Year: 2023 · PMID: 37283696

  11. 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

  12. 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

  13. 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: 725

  14. 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

  15. 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

  16. 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: 20

  17. 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

  18. DOCKGROUND membrane protein-protein set

    Kotthoff I, Kundrotas PJ, Vakser IA

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

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

    Pozzati G, Kundrotas P, Elofsson A

    Proteins · Year: 2022 · PMID: 35246997 · Citations: 8

  20. Dockground scoring benchmarks for protein docking

    Kotthoff I, Kundrotas PJ, Vakser IA

    Proteins · Year: 2022 · PMID: 35072956 · Citations: 5

  21. 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

  22. 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: 137

  23. 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

  24. 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

  25. 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: 13

  26. Application of docking methodologies to modeled proteins

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

    Proteins · Year: 2020 · PMID: 32170770 · Citations: 45

  27. 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: 12

  28. 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: 142

  29. 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

  30. 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: 21

  31. 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: 26

  32. 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: 6

  33. 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: 39

  34. 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

  35. 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: 107

  36. Structural quality of unrefined models in protein docking

    Anishchenko I, Kundrotas PJ, Vakser IA

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

  37. Modeling complexes of modeled proteins

    Anishchenko I, Kundrotas PJ, Vakser IA

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

  38. Template-Based Modeling of Protein-RNA Interactions

    Zheng J, Kundrotas PJ, Vakser IA, Liu S

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

  39. 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: 175

  40. Text Mining for Protein Docking

    Badal VD, Kundrotas PJ, Vakser IA

    PLoS computational biology · Year: 2015 · PMID: 26650466 · Citations: 23

  41. 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

  42. Protein models docking benchmark 2

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

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

  43. Structural templates for comparative protein docking

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

    Proteins · Year: 2015 · PMID: 25488330 · Citations: 35

  44. 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

  45. Protein models: the Grand Challenge of protein docking

    Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA

    Proteins · Year: 2014 · PMID: 23934791 · Citations: 36

  46. Structural templates for modeling homodimers

    Kundrotas PJ, Vakser IA, Janin J

    Protein science : a publication of the Protein Society · Year: 2013 · PMID: 23996787 · Citations: 22

  47. 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

  48. 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

  49. 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

  50. 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: 237

  51. 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

  52. Docking by structural similarity at protein-protein interfaces

    Sinha R, Kundrotas PJ, Vakser IA

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

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

    Kundrotas PJ, Vakser IA

    PLoS computational biology · Year: 2010 · PMID: 20369011 · Citations: 50

  54. GWIDD: Genome-wide protein docking database

    Kundrotas PJ, Zhu Z, Vakser IA

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

  55. 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: 68

  56. 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: 65

  57. Predicting 3D structures of protein-protein complexes

    Vakser IA, Kundrotas P

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

  58. Predicting interacting and interfacial residues using continuous sequence segments

    Kundrotas P, Alexov E

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

  59. 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

  60. 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

  61. 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

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

    Kundrotas PJ, Alexov E

    Nucleic acids research · Year: 2007 · PMID: 17071962 · Citations: 69

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

    Kundrotas PJ, Alexov EG

    BMC bioinformatics · Year: 2006 · PMID: 17109752 · Citations: 62

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

    Kundrotas PJ, Alexov E

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

  65. Electrostatic properties of protein-protein complexes

    Kundrotas PJ, Alexov E

    Biophysical journal · Year: 2006 · PMID: 16782791 · Citations: 117

  66. Statistical studies of flexible nonhomogeneous polypeptide chains

    Kundrotas PJ

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

  67. Charge sequence coding in statistical modeling of unfolded proteins

    Kundrotas PJ, Karshikoff A

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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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: 13

  73. 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

  74. 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

  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: 0

  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: 14

  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: 10

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

    Dourado DF, Flores SC

    Scientific reports · Year: 2016 · PMID: 27173910 · Citations: 20

  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: 36

  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: 96

  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: 117

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

    Dourado DF, Flores SC

    Proteins · Year: 2014 · PMID: 24975440 · Citations: 71

  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: 116

  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: 349

  22. Multiscale modeling of macromolecular biosystems

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

    Briefings in bioinformatics · Year: 2012 · PMID: 22228511 · Citations: 40

  23. Predicting protein ligand binding motions with the conformation explorer

    Flores SC, Gerstein MB

    BMC bioinformatics · Year: 2011 · PMID: 22032721 · Citations: 18

  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: 77

  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: 63

  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: 96

  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: 52

  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: 39

  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: 183

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: 1

Query: "Viliuga V"[Author] | Publications: 6 | Citation matches: 6 | Scholar | ORCID

  1. ABAG-Rank: Improving Model Selection of AlphaFold Antibody-Antigen Complexes by Learning to Rank

    M Tadiello, M Ludaic, V Viliuga, A Elofsson

    bioRxiv preprint · Year: 2026 · Citations: 0

  2. 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: 3

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

    KT Korbeld*, V Viliuga*, M Fürst

    bioRxiv preprint · Year: 2025 · Citations: 1

  4. Learning conformational ensembles of proteins based on backbone geometry

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

    arXiv preprint · Year: 2025 · Citations: 5

  5. Flexibility-conditioned protein structure design with flow matching

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

    arXiv preprint · Year: 2025 · Citations: 6

  6. 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: 4

Query: "Ludaic M"[Author] | Publications: 1 | Citation matches: 0 | ORCID

  1. 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. ABAG-Rank: Improving Model Selection of AlphaFold Antibody-Antigen Complexes by Learning to Rank

    M Tadiello, M Ludaic, V Viliuga, A Elofsson

    bioRxiv 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: 4

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

Query: "Goldtzvik, Yonathan"[Author] | Publications: 9 | Citation matches: 9 | Scholar | ORCID

  1. AlphaFold Database expands to proteome-scale quaternary structures

    Y Han, MI Tsenkov, NAE Venanzi, D Bertoni, S Cha, A Chacon, N Dietrich, ...

    bioRxiv preprint · Year: 2026 · Citations: 2

  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: 51

  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: 3

  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: 19

  7. Dynamics of Allosteric Transitions in Dynein

    Goldtzvik Y, Mugnai ML, Thirumalai D

    Structure (London, England : 1993) · Year: 2018 · PMID: 30270176 · Citations: 20

  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: 36

  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: 19

Query: "Panconi L"[Author] | Publications: 7 | Citation matches: 7 | Scholar | ORCID

  1. Nanoscale protein clustering modulates the input-output response of cellular signalling pathways

    L Panconi, J Griffié, DM Owen

    bioRxiv preprint · Year: 2025 · Citations: 0

  2. 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: 1

  3. 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: 18

  4. 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: 4

  5. 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: 3

  6. 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: 12

  7. 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: 2

  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: 1

  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: 16