MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W549-55. doi: 10.1093/nar/gkm266. Epub 2007 May 3.


MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases. The available crystal structures of protein-peptide complexes in PDB are used as templates for modeling peptides of desired sequence in the substrate-binding pocket of MHCs or protein kinases. The substrate peptides are modeled using the same backbone conformation as in the template and the side-chain conformations are obtained by the program SCWRL. MODPROPEP provides a number of user-friendly interfaces for visualizing the structure of the modeled protein-peptide complexes and analyzing the contacts made by the modeled peptide ligand in the substrate-binding pocket of the MHC or protein kinase. Analysis of these specific inter-molecular contacts is crucial for understanding structural basis of the substrate specificity of these two protein families. This software also provides appropriate interfaces for identifying, putative MHC-binding peptides in the sequence of an antigen or phosphorylation sites on the substrate protein of a kinase, by scoring these inter-molecular contacts using residue-based statistical pair potentials. MODPROPEP would complement various available sequence-based programs (SYFPEITHI, SCANSITE, etc.) for predicting substrates of MHCs and protein kinases. The program is available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Computational Biology / methods*
  • Computer Simulation
  • Crystallography, X-Ray
  • Databases, Protein
  • Humans
  • Internet
  • Major Histocompatibility Complex
  • Peptides / chemistry*
  • Protein Conformation
  • Proteins / chemistry*
  • Software*
  • User-Computer Interface


  • Peptides
  • Proteins