MODPROPEP uses the available crystal structures of protein-peptide complexes (involving MHCs and protein kinases) in PDB as structural templates for modeling complexes involving peptides of desired sequence. The modeling of the peptides in the substrate binding pocket of the MHC or protein kinase molecules is carried out by using the same backbone conformation as the template and building the side chains by the program SCWRL, which uses a rotamer library approach.
MODPROPEP provides a number of user friendly interfaces for visualizing the structure of the modeled protein-peptide complex and analyzing the contacts made by the modeled peptide ligand in various subsites of the substrate binding pocket of the MHC or protein kinase. Analysis of these specific intermolecular contacts is crucial for understanding structural basis of the substrate specificity of these two protein families. This software also provides appropriate interfaces for scoring the relative binding affinity of a set of peptides using residue based statistical pair potentials. This option would help the user in identifying, putative MHC binding peptides in the sequence of an antigen or phosphorylation sites on the substrate protein of a protein kinase.
MODPROPEP would complement various available sequence based programs (SYFPEITHI, SCANSITE etc) for predicting substrates of MHC and protein kinases. It will be a valuable resource for design of MHC binding peptides and deciphering substrate specificity of large number of protein kinases found in newly sequenced genomes.