Our ambition is to develop better methods for prediction of protein structure and function.
The most successful methods are provided as web-based servers.

Git repositories

Web-services developed through EMBRACE

  • Pfrag: a program for homology modelling
  • SHRIMP: a program for Hidden Markov Model-based homology scoring

Structure Predictions

  • PconsD: ultra rapid, accurate model quality assessment for protein structure prediction.
  • PconsC: combination of direct information methods and alignments improves contact prediction.
  • PconsC2: Improved contact predictions using the recognition of protein like contact patterns
  • The Pcons meta and consensus server. Now it also builds very nice homology models in less than a minute .
  • ProQ: a predictor of protein quality.
  • TOBMODEL: automatic modelling of beta-barrel membrane proteins.

Membrane Protein Topology Prediction Methods

  • TOPCONS: A new consensus method to predict the topology of membrane proteins. Now features signal protein prediction and uses a very fast method to create profiles that enables prediction of entire genomes.
  • TOPCONS-single: a consensus method for topology prediction of alpha-helical membrane proteins, but without the need for BLAST runs. It is based on several tools that accept a single protein sequence as input. Ideal for a quick scan of entire genomes.
  • SCAMPI: topology predictor for beta-barrel membrane proteins. Ideal for a quick scan of very large datasets.
  • BOCTOPUS: topology predictor for beta-barrel membrane proteins
  • OCTOPUS & SPOCTOPUS: prediction of membrane protein topology and signal peptides
  • ZPRED: prediction of TransMembrane Regions and distance to the membrane center (available through the TOPCONS webserver)
  • DAS: prediction of TransMembrane Regions.

Subcellular Localization Prediction Methods

  • SubCons: a new ensemble method for improved human subcellular localization predictions.
  • Pmembr: a threading method for membrane proteins.
  • Palign: a program for sequence alignments


  • SVMHC: prediction of MHC class I binding peptides.
  • PhylProM: phylogenetic profiles
  • PeroxiP: prediction of peroxisomal proteins