title: MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes.
abstract: 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 http://www.nii.res.in/modpropep.html.
authors.affiliation: National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Narendra
authors.initials: N
authors.lastname: Kumar
authors.forename: Debasisa
authors.initials: D
authors.lastname: Mohanty
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008285:Major Histocompatibility Complex; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D011506:Proteins