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

What you can do:
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.
  • Major Histocompatibility Complex
  • Peptides
  • Protein Conformation
  • protein-peptide complexes
  • protein-peptide
  • peptide
  • MHC
  • protein kinase
This record last updated: 06-02-2008
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