ArticleNucleic acids research2007
MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 37 citations in OpenAlex.
- Strategies for neoantigen screening and immunogenicity validation in cancer immunotherapy (Review).International journal of oncology · 2025Review
- A Pan-Specific GRU-Based Recurrent Neural Network for Predicting HLA-I-Binding Peptides.ACS omega · 2020Article
- Rapid microsphere-assisted peptide screening (MAPS) of promiscuous MHCII-binding peptides in Zika virus envelope protein.AIChE journal. American Institute of Chemical Engineers · 2020Article
- Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.Current topics in medicinal chemistry · 2018Review
- modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks.Biology direct · 2016Article
- Understanding the molecular basis of substrate binding specificity of PTB domains.Scientific reports · 2016Article
- Computer-aided vaccine designing approach against fish pathogens Edwardsiella tarda and Flavobacterium columnare using bioinformatics softwares.Drug design, development and therapy · 2016Article
- Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases.Science signaling · 2015Article
- Machine Learning Methods for Predicting HLA-Peptide Binding Activity.Bioinformatics and biology insights · 2015Review
- HLA-B*27 subtype specificity determines targeting and viral evolution of a hepatitis C virus-specific CD8+ T cell epitope.Journal of hepatology · 2014Article
- Genome-wide structural modelling of TCR-pMHC interactions.BMC genomics · 2013Article
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- Resistance-associated epitopes of HIV-1C-highly probable candidates for a multi-epitope vaccine.Immunogenetics · 2012Article
- Article
- CTL recognition of a novel HLA-A*0201-binding peptide derived from glioblastoma multiforme tumor cells.Cancer immunology, immunotherapy : CII · 2011Article
- PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes.Nucleic acids research · 2011Article
- Predicting peptide binding affinities to MHC molecules using a modified semi-empirical scoring function.PloS one · 2011Article
- Chk1-dependent constitutive phosphorylation of BLM helicase at serine 646 decreases after DNA damage.Molecular cancer research : MCR · 2010Article
- Understanding the focused CD4 T cell response to antigen and pathogenic organisms.Immunologic research · 2009Review
- Four distances between pairs of amino acids provide a precise description of their interaction.PLoS computational biology · 2009Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.