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Peptide binding specificity prediction using fine-tuned protein structure prediction networks [article]

Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad Abedi, David Baker, Philip Harlan Bradley
2022 bioRxiv   pre-print
generalizable performance on a wide range of Class I and Class II peptide-MHC interactions that approaches the overall performance of the state-of-the-art NetMHCpan sequence-based method.  ...  The peptide-MHC optimized model shows excellent performance in distinguishing binding and non-binding peptides to SH3 and PDZ domains.  ...  This work was supported with  ... 
doi:10.1101/2022.07.12.499365 fatcat:rjlae5onvbdw3h6p6oyiswnjfm

Towards Universal Structure-Based Prediction of Class II MHC Epitopes for Diverse Allotypes

Andrew J. Bordner, Richard James Morris
2010 PLoS ONE  
We also discuss how accounting for peptide binding in multiple registers to class II MHC largely explains the systematically worse performance of prediction methods for class II MHC compared with those  ...  for class I MHC based on quantitative prediction performance estimates for peptide binding to class II MHC in a fixed register.  ...  Mittelmann for helping with the MultiRTA calculations and Molsoft LLC for kindly providing the ICM molecular modeling software used in this study.  ... 
doi:10.1371/journal.pone.0014383 pmid:21187956 pmcid:PMC3004863 fatcat:nqb7lfb52zex7mjkrsofj5neue

Methods and protocols for prediction of immunogenic epitopes

J. C. Tong, T. W. Tan, S. Ranganathan
2006 Briefings in Bioinformatics  
The most important bioinformatics tools and methods with relevance to the study of peptide/MHC interactions have been reviewed.  ...  This article examines existing computational strategies for the study of peptide/MHC interactions.  ...  peptides, and those that employ three-dimensional (3D) structures to model peptide/MHC interactions.  ... 
doi:10.1093/bib/bbl038 pmid:17077136 fatcat:w6une7hwyrev5m3ocvqwjlj7am

A general model of invariant chain association with class II major histocompatibility complex proteins

C. Lee, H. M. McConnell
1995 Proceedings of the National Academy of Sciences of the United States of America  
We have employed molecular modeling to predict the structure of class 11-associated invariant chain peptide (CLIP)-MHC protein complexes and to ask whether the predicted mode of association could be general  ...  Our model predicts the burial of CLIP residues in the deep P1 and P9 anchor pockets and other detailed interactions, which we have compared with available data.  ...  To investigate the hypothesis that CLIP might bind in a general way across all class II MHC proteins, we have modeled CLIP with the murine class II I-Ak, I-Au, and I-Ad, whose structures have been modeled  ... 
doi:10.1073/pnas.92.18.8269 pmid:7667280 pmcid:PMC41138 fatcat:ahyc6nt7bzcolgm2v6mqb2jl44

Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

Hao Zhang, Peng Wang, Nikitas Papangelopoulos, Ying Xu, Alessandro Sette, Philip E. Bourne, Ole Lund, Julia Ponomarenko, Morten Nielsen, Bjoern Peters, Narcis Fernandez-Fuentes
2010 PLoS ONE  
We here implemented and evaluated three prediction methods for MHC class II molecules: statistical potentials derived from the analysis of known protein structures; energetic evaluation of different peptide  ...  Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide  ...  in 3D structures of peptides in complexes with MHC class II of a particular allele.  ... 
doi:10.1371/journal.pone.0009272 pmid:20174654 pmcid:PMC2822856 fatcat:wvctr64b4nh6ri2tivm45i3q2e

Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders

Rodrigo Ochoa, Roman A. Laskowski, Janet M. Thornton, Pilar Cossio
2021 Frontiers in Molecular Biosciences  
The prediction of peptide binders to Major Histocompatibility Complex (MHC) class II receptors is of great interest to study autoimmune diseases and for vaccine development.  ...  We modelled a set of 837 peptides bound to an MHC class II allele, and optimized the sampling of the conformations using the Rosetta backrub method by comparing the results to molecular dynamics simulations  ...  We modelled a large set of peptides with binding data available for one representative MHC class II allele.  ... 
doi:10.3389/fmolb.2021.636562 fatcat:jilborinmrdjzdorubpykjv3ly

AN IMMUNOINFORMATICS STUDY TO PREDICT EPITOPES IN THE ENVELOPE PROTEIN OF SARS-COV-2 [article]

Renu Jakhar, S.K GAKHAR
2020 bioRxiv   pre-print
CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19.  ...  Then we docked the best predicted CTL epitopes with HLA alleles.  ...  Regarding T cell, the FLAFVVFLL epitope was highly recommended as a therapeutic peptide vaccine to interact with both MHC class I and II.  ... 
doi:10.1101/2020.05.26.115790 fatcat:ztekpcje3nf5djors4bsg34aw4

A Novel Predictive Technique for the MHC Class II Peptide-Binding Interaction

Matthew N Davies, Clare E Sansom, Claude Beazley, David S Moss
2003 Molecular Medicine  
We have developed a novel predictive technique that uses molecular modeling of predetermined crystal structures to estimate the stability of an MHC Class II peptide complex.  ...  Various predictive algorithms have been developed to estimate a peptide's capacity to form a stable complex with a given MHC Class II allele, a technique integral to the strategy of vaccine design.  ...  We have developed this technique as a novel method of modeling the MHC Class II peptide-binding interaction.  ... 
doi:10.2119/2003-00032.sansom fatcat:oxyet4tg7nhlpmcoxtgbxn3ase

An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-CoV-2

Renu Jakhar, S. K. Gakhar, Louis Detolla
2020 Canadian Journal of Infectious Diseases and Medical Microbiology  
The predicted HTL and CTL epitopes were docked with HLA alleles and binding energies were evaluated.  ...  We aimed at designing a peptide vaccine for COVID-19 particularly for the envelope protein using computational methods to predict epitopes inducing the immune system.  ...  Prediction of Helper T-Lymphocyte Epitopes and Interaction with MHC Class II.  ... 
doi:10.1155/2020/7079356 pmid:33299503 pmcid:PMC7686850 fatcat:hm4t77cb7ncqbpp5zm66quvume

T-cell epitope vaccine design by immunoinformatics

A. Patronov, I. Doytchinova
2013 Open Biology  
virus protein proteasome endosome peptide fragments MHC class I MHC class II invariant chain endoplasmic reticulum TAP cytosol antigenic peptides CLIP class II class I  ...  [136] generated MHC class II models by evaluating the contribution of a given amino acid to the overall peptide affinity.  ... 
doi:10.1098/rsob.120139 pmid:23303307 pmcid:PMC3603454 fatcat:7jqqswcnafailh5r4p2wqnkgha

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

N. Kumar, D. Mohanty
2007 Nucleic Acids Research  
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.  ...  Dunbrack Jr for allowing the use of SCWRL for modeling of side chains.  ... 
doi:10.1093/nar/gkm266 pmid:17478500 pmcid:PMC1933231 fatcat:74jtt2fb5jertin2q7fyuxfkxa

Trans-allelic model for prediction of peptide:MHC-II interactions [article]

A. M. Degoot, Faraimunashe Chirove, Wilfred Ndifon
2017 arXiv   pre-print
In this paper, we present a comprehensive trans-allelic prediction model, a generalized version of our previous biophysical model, that can predict peptide interactions for all three human MHC-II loci  ...  (HLA-DR, HLA-DP and HLA-DQ), using both peptide sequence data and structural information of MHC-II molecules.  ...  In this study we have developed a trans-allelic model that can predict peptide interactions to the three human MHC-II loci.  ... 
arXiv:1712.00351v1 fatcat:odsh3jc2t5gqtlodqa6okoxdii

Trans-Allelic Model for Prediction of Peptide:MHC-II Interactions

Abdoelnaser M. Degoot, Faraimunashe Chirove, Wilfred Ndifon
2018 Frontiers in Immunology  
In this article, we present a comprehensive transallelic prediction model, a generalized version of our previous biophysical model, that can predict peptide interactions for all three human MHC-II loci  ...  (HLA-DR, HLA-DP, and HLA-DQ), using both peptide sequence data and structural information of MHC-II molecules.  ...  This flexible constraint on peptide lengths together with its immense polymorphism, contribute to a lower predictive performance of computational methods for peptide-MHC-II interactions compared with MHC-I  ... 
doi:10.3389/fimmu.2018.01410 pmid:29988560 pmcid:PMC6026802 fatcat:dpnm6ytponbv3apaqopnz3kbxu

Modeling the structure of bound peptide ligands to major histocompatibility complex

Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan
2004 Protein Science  
In the first test, 33 out of 40 MHC class I and class II peptides and in the second test, 11 out of 15 MHC-peptide complexes were modeled with a C␣ RMSD < 1.00 Å.  ...  In this article, we present a new technique for the rapid and precise docking of peptides to MHC class I and class II receptors.  ...  This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.  ... 
doi:10.1110/ps.04631204 pmid:15322290 pmcid:PMC2279999 fatcat:yhdcyqgojvf7njpbpfo7z6jnvy

Molecular Modeling and Design of Invariant Chain Peptides with Altered Dissociation Kinetics from Class II MHC†

Michael N. Liang, Christopher Lee, Yu Xia, Harden M. McConnell
1996 Biochemistry  
We have used molecular modeling to design substitutions in an invariant chain-derived peptide (CLIP), so as to alter the stability of its complex with class II major histocompatibility complex (MHC) proteins  ...  We sought first to test whether CLIP binds in the same way to different class II MHC proteins.  ...  Peptide backbone coordinates of the hemagglutinin 306-318 peptide, from the crystal structure of its complex with the class II MHC protein HLA-DR1 , were superimposed on our A u and A k models, as a canonical  ... 
doi:10.1021/bi961725b pmid:8942634 fatcat:lwf3jqm5sjgrjn6evpw63lnapq
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