Cargando…

DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction

MOTIVATION: Computationally predicting major histocompatibility complex class I (MHC-I) peptide binding affinity is an important problem in immunological bioinformatics, which is also crucial for the identification of neoantigens for personalized therapeutic cancer vaccines. Recent cutting-edge deep...

Descripción completa

Detalles Bibliográficos
Autores principales:	Qu, Wei, You, Ronghui, Mamitsuka, Hiroshi, Zhu, Shanfeng
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Original Paper
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10516514/ https://www.ncbi.nlm.nih.gov/pubmed/37669154 http://dx.doi.org/10.1093/bioinformatics/btad551

Ejemplares similares

DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction
por: You, Ronghui, et al.
Publicado: (2022)

MetaMHC: a meta approach to predict peptides binding to MHC molecules
por: Hu, Xihao, et al.
Publicado: (2010)

DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction
por: You, Ronghui, et al.
Publicado: (2021)

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing
por: Peng, Shengwen, et al.
Publicado: (2016)

Partial Dissociation of Truncated Peptides Influences the Structural Dynamics of the MHCI Binding Groove
por: Fisette, Olivier, et al.
Publicado: (2017)

DeepLigand: accurate prediction of MHC class I ligands using peptide embedding
por: Zeng, Haoyang, et al.
Publicado: (2019)

High-affinity CD8 variants enhance the sensitivity of pMHCI antigen recognition via low-affinity TCRs
por: Knezevic, Lea, et al.
Publicado: (2023)

CD8(+) T-cell specificity is compromised at a defined MHCI/CD8 affinity threshold
por: Dockree, Tamsin, et al.
Publicado: (2017)

NetGO: improving large-scale protein function prediction with massive network information
por: You, Ronghui, et al.
Publicado: (2019)

Individual MHCI-Restricted T-Cell Receptors are Characterized by a Unique Peptide Recognition Signature
por: Wooldridge, Linda
Publicado: (2013)

High-Throughput, Quantitative Analysis of Peptide-Exchanged MHCI Complexes by Native Mass Spectrometry
por: Schachner, Luis F., et al.
Publicado: (2022)

MHC2SKpan: a novel kernel based approach for pan-specific MHC class II peptide binding prediction
por: Guo, Linyuan, et al.
Publicado: (2013)

Predicting MHC-peptide binding affinity by differential boundary tree
por: Feng, Peiyuan, et al.
Publicado: (2021)

TEPITOPEpan: Extending TEPITOPE for Peptide Binding Prediction Covering over 700 HLA-DR Molecules
por: Zhang, Lianming, et al.
Publicado: (2012)

Coreceptor affinity for MHC defines peptide specificity requirements for TCR interaction with coagonist peptide–MHC
por: Hoerter, John A.H., et al.
Publicado: (2013)

Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity
por: Davies, Matthew N, et al.
Publicado: (2006)

Binding peptide generation for MHC Class I proteins with deep reinforcement learning
por: Chen, Ziqi, et al.
Publicado: (2023)

MHC2MIL: a novel multiple instance learning based method for MHC-II peptide binding prediction by considering peptide flanking region and residue positions
por: Xu, Yichang, et al.
Publicado: (2014)

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11
por: Lundegaard, Claus, et al.
Publicado: (2008)

TCR‐induced alteration of primary MHC peptide anchor residue
por: Madura, Florian, et al.
Publicado: (2019)

Accurate modeling of peptide-MHC structures with AlphaFold
por: Mikhaylov, Victor, et al.
Publicado: (2023)

Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins
por: Frietze, Karla K., et al.
Publicado: (2016)

DeepDTA: deep drug–target binding affinity prediction
por: Öztürk, Hakime, et al.
Publicado: (2018)

Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction
por: Han, Youngmahn, et al.
Publicado: (2017)

MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model
por: Venkatesh, Gopalakrishnan, et al.
Publicado: (2020)

ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network
por: Wang, Ziye, et al.
Publicado: (2021)

Viral MHCI inhibition evades tissue-resident memory T cell formation and responses
por: Lauron, Elvin J., et al.
Publicado: (2019)

PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes
por: Marzella, Dario F., et al.
Publicado: (2022)

Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model
por: Bordner, Andrew J, et al.
Publicado: (2010)

Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation
por: Mohseni Behbahani, Yasser, et al.
Publicado: (2023)

Application of a New Probabilistic Model for Mining Implicit Associated Cancer Genes from OMIM and Medline
por: Zhu, Shanfeng, et al.
Publicado: (2007)

Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer
por: Liao, Zhirui, et al.
Publicado: (2022)

Progranulin mediates immune evasion of pancreatic ductal adenocarcinoma through regulation of MHCI expression
por: Cheung, Phyllis F., et al.
Publicado: (2022)

Structural basis for ineffective T-cell responses to MHC anchor residue-improved “heteroclitic” peptides
por: Madura, Florian, et al.
Publicado: (2015)

Peptide length significantly influences in vitro affinity for MHC class II molecules
por: O'Brien, Cathal, et al.
Publicado: (2008)

Predicting Peptide Binding Affinities to MHC Molecules Using a Modified Semi-Empirical Scoring Function
por: Liao, Webber W. P., et al.
Publicado: (2011)

In silico design of MHC class I high binding affinity peptides through motifs activation map
por: Xiao, Zhoujian, et al.
Publicado: (2018)

DeepACP: A Novel Computational Approach for Accurate Identification of Anticancer Peptides by Deep Learning Algorithm
por: Yu, Lezheng, et al.
Publicado: (2020)

Identification of human viral protein-derived ligands recognized by individual MHCI-restricted T-cell receptors
por: Szomolay, Barbara, et al.
Publicado: (2016)

Structural Basis for the Restoration of TCR Recognition of an MHC Allelic Variant by Peptide Secondary Anchor Substitution
por: Miley, Michael J., et al.
Publicado: (2004)

Cannot write session to /tmp/vufind_sessions/sess_5pcfalgis036tfl41sq3f7cpck