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

@article{citeulike:2237066, 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.}, address = {National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.}, author = {Kumar, N. and Mohanty, D. }, citeulike-article-id = {2237066}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {binding, complex, kinase, mhc, peptide, protein-protein, software, webserver}, month = {July}, number = {Web Server issue}, posted-at = {2008-01-16 02:50:32}, priority = {2}, title = {MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/17478500}, volume = {35}, year = {2007} }

TY - JOUR ID - citeulike:2237066 L3 - citeulike-article-id:2237066 TI - MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. JF - Nucleic Acids Res VL - 35 IS - Web Server issue AD - National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India. SN - 1362-4962 N2 - 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. KW - binding KW - complex KW - kinase KW - mhc KW - peptide KW - protein-protein KW - software KW - webserver AU - Kumar, N AU - Mohanty, D PY - 2007/07/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/17478500 ER -