Cargando…

3pHLA-score improves structure-based peptide-HLA binding affinity prediction

Binding of peptides to Human Leukocyte Antigen (HLA) receptors is a prerequisite for triggering immune response. Estimating peptide-HLA (pHLA) binding is crucial for peptide vaccine target identification and epitope discovery pipelines. Computational methods for binding affinity prediction can accel...

Descripción completa

Detalles Bibliográficos
Autores principales:	Conev, Anja, Devaurs, Didier, Rigo, Mauricio Menegatti, Antunes, Dinler Amaral, Kavraki, Lydia E.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2022
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9232595/ https://www.ncbi.nlm.nih.gov/pubmed/35750701 http://dx.doi.org/10.1038/s41598-022-14526-x

Ejemplares similares

HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy
por: Antunes, Dinler A., et al.
Publicado: (2020)

SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development
por: Rigo, Mauricio Menegatti, et al.
Publicado: (2022)

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
por: Conev, Anja, et al.
Publicado: (2023)

PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure
por: Hall-Swan, Sarah, et al.
Publicado: (2023)

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
por: Conev, Anja, et al.
Publicado: (2023)

General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept
por: Antunes, Dinler A., et al.
Publicado: (2018)

Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G
por: Arns, Thais, et al.
Publicado: (2020)

Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data
por: Devaurs, Didier, et al.
Publicado: (2018)

Computational analysis of complement inhibitor compstatin using molecular dynamics
por: Devaurs, Didier, et al.
Publicado: (2020)

DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins
por: Hall-Swan, Sarah, et al.
Publicado: (2021)

TCR mimic compounds for pHLA targeting with high potency modalities in oncology
por: Gerber, Hans-Peter, et al.
Publicado: (2022)

Large-Scale Structure-Based Screening of Potential T Cell Cross-Reactivities Involving Peptide-Targets From BCG Vaccine and SARS-CoV-2
por: Tarabini, Renata Fioravanti, et al.
Publicado: (2022)

Sulfamethoxazole Induces a Switch Mechanism in T Cell Receptors Containing TCRVβ20-1, Altering pHLA Recognition
por: Watkins, Stephan, et al.
Publicado: (2013)

Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data
por: Devaurs, Didier, et al.
Publicado: (2017)

Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins
por: Devaurs, Didier, et al.
Publicado: (2019)

Structural basis of the TCR-pHLA complex provides insights into the unconventional recognition of CDR3β in TCR cross-reactivity and alloreactivity
por: San, Dan, et al.
Publicado: (2022)

CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes
por: Sinigaglia, Marialva, et al.
Publicado: (2013)

Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests
por: Abella, Jayvee R., et al.
Publicado: (2020)

The hemolytic and cytolytic activities of Serratia marcescens phospholipase A (PhlA) depend on lysophospholipid production by PhlA
por: Shimuta, Ken, et al.
Publicado: (2009)

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations
por: Abella, Jayvee R., et al.
Publicado: (2019)

Cancer vaccines based on whole-tumor lysate or neoepitopes with validated HLA binding outperform those with predicted HLA-binding affinity
por: Fritah, Hajer, et al.
Publicado: (2023)

PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity
por: Liu, Geng, et al.
Publicado: (2017)

The increased ability to present citrullinated peptides is not unique to HLA-SE molecules: arginine-to-citrulline conversion also enhances peptide affinity for HLA-DQ molecules
por: Kampstra, Arieke S. B., et al.
Publicado: (2016)

Designing high affinity target-binding peptides to HLA-E: a key membrane antigen of multiple myeloma
por: Yang, Ying, et al.
Publicado: (2020)

DockTope: a Web-based tool for automated pMHC-I modelling
por: Menegatti Rigo, Maurício, et al.
Publicado: (2015)

Interaction of Nevirapine with the Peptide Binding Groove of HLA-DRB1*01:01 and Its Effect on the Conformation of HLA-Peptide Complex
por: Hirasawa, Makoto, et al.
Publicado: (2018)

On the peptide binding affinity changes in population-specific HLA repertoires to the SARS-CoV-2 variants Delta and Omicron
por: Chen, Lu-Chun, et al.
Publicado: (2022)

A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction
por: Kravchenko, Oleksandr, et al.
Publicado: (2020)

T-Epitope Designer: A HLA-peptide binding prediction server
por: Kangueane, Pandjassarame, et al.
Publicado: (2005)

Evidence of widespread binding of HLA class I molecules to peptides
Publicado: (1990)

Peptide binding predictions for HLA DR, DP and DQ molecules
por: Wang, Peng, et al.
Publicado: (2010)

Machine Learning Methods for Predicting HLA–Peptide Binding Activity
por: Luo, Heng, et al.
Publicado: (2015)

Identification of the core regulators of the HLA I-peptide binding process
por: Zhang, Yu-Hang, et al.
Publicado: (2017)

Integrating In Silico and In Vitro Analysis of Peptide Binding Affinity to HLA-Cw*0102: A Bioinformatic Approach to the Prediction of New Epitopes
por: Walshe, Valerie A., et al.
Publicado: (2009)

The inter-locus recombinant HLA-B*4601 has high selectivity in peptide binding and functions characteristic of HLA-C
Publicado: (1996)

Human histocompatibility leukocyte antigen (HLA)-DM edits peptides presented by HLA-DR according to their ligand binding motifs
Publicado: (1996)

Lymphocyte proliferation induced by high-affinity peptides for HLA-B*51:01 in Behçet’s uveitis
por: Kaburaki, Toshikatsu, et al.
Publicado: (2019)

Mass spectrometry-assisted identification of ADAMTS13-derived peptides presented on HLA-DR and HLA-DQ
por: Hrdinová, Johana, et al.
Publicado: (2018)

Canonical and Cross-reactive Binding of NK Cell Inhibitory Receptors to HLA-C Allotypes Is Dictated by Peptides Bound to HLA-C
por: Sim, Malcolm J. W., et al.
Publicado: (2017)

Prediction of HLA-A2 binding peptides using Bayesian network
por: Astakhov, Vadim, et al.
Publicado: (2005)

Cannot write session to /tmp/vufind_sessions/sess_s3o4fflc2ebppvnvpqenn1c7vf