and Debasisa Mohanty
National Institute of Immunology
MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with 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.