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.
Highlights:
- 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.
Keywords:
- Major Histocompatibility Complex
- Peptides
- Protein Conformation
- protein-peptide complexes
- protein-peptide
- peptide
- MHC
- protein kinase
Literature & Tutorials:
This record last updated: 06-02-2008