Cargando…

BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning

MOTIVATION: Increasingly comprehensive characterization of cancer-associated genetic alterations has paved the way for the development of highly specific therapeutic vaccines. Predicting precisely the binding and presentation of peptides to major histocompatibility complex (MHC) alleles is an import...

Descripción completa

Detalles Bibliográficos
Autores principales:	Cheng, Jun, Bendjama, Kaïdre, Rittner, Karola, Malone, Brandon
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Original Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9502151/ https://www.ncbi.nlm.nih.gov/pubmed/34096999 http://dx.doi.org/10.1093/bioinformatics/btab422

Ejemplares similares

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)

Thermodynamics of Peptide-MHC Class II Interactions: Not all Complexes are Created Equal
por: Ferrante, Andrea
Publicado: (2013)

Sequential administration of MVA-based vaccines and PD-1/PD-L1-blocking antibodies confers measurable benefits on tumor growth and survival: Preclinical studies with MVA-βGal and MVA-MUC1 (TG4010) in a murine tumor model
por: Remy-Ziller, Christelle, et al.
Publicado: (2017)

Motifs and supermotifs for MHC class II binding peptides
Publicado: (1995)

Model for the Peptide-Free Conformation of Class II MHC Proteins
por: Painter, Corrie A., et al.
Publicado: (2008)

Regulation of MHC Class II-Peptide Complex Expression by Ubiquitination
por: Cho, Kyung-Jin, et al.
Publicado: (2013)

Prediction of MHC class II binding peptides based on an iterative learning model
por: Murugan, Naveen, et al.
Publicado: (2005)

Instance Sequence Queries for Video Instance Segmentation with Transformers
por: Xu, Zhujun, et al.
Publicado: (2021)

Identical peptides recognized by MHC class I- and II-restricted T cells
Publicado: (1989)

Design of Peptide Immunotherapies for MHC Class-II-Associated Autoimmune Disorders
por: Fridkis-Hareli, Masha
Publicado: (2013)

The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding
por: Shen, Wen-Jun, et al.
Publicado: (2018)

A Missing Switch in Peptide Exchange for MHC Class II Molecules
por: Freund, Christian, et al.
Publicado: (2019)

Structural Properties of MHC Class II Ligands, Implications for the Prediction of MHC Class II Epitopes
por: Jørgensen, Kasper Winther, et al.
Publicado: (2010)

HLA-DM catalytically enhances peptide dissociation by sensing peptide–MHC class II interactions throughout the peptide-binding cleft
por: Reyes-Vargas, Eduardo, et al.
Publicado: (2020)

Ligation of MHC Class II Induces PKC-Dependent Clathrin-Mediated Endocytosis of MHC Class II
por: Masaki, Kento, et al.
Publicado: (2020)

MHC class I and MHC class II reporter mice enable analysis of immune oligodendroglia in mouse models of multiple sclerosis
por: Harrington, Em P, et al.
Publicado: (2023)

Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for presentation of transformed self
por: Mohammed, Fiyaz, et al.
Publicado: (2008)

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

Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
por: Zhang, Hao, et al.
Publicado: (2010)

Citrullination only infrequently impacts peptide binding to HLA class II MHC
por: Sidney, John, et al.
Publicado: (2017)

Superantigen and class II MHC molecules.
por: Kim, J.
Publicado: (1995)

Organizing MHC Class II Presentation
por: Fooksman, David R.
Publicado: (2014)

MHC Class II Presentation in Autoimmunity
por: Ishina, Irina A., et al.
Publicado: (2023)

The impact of DM on MHC class II–restricted antigen presentation can be altered by manipulation of MHC–peptide kinetic stability
por: Lazarski, Christopher A., et al.
Publicado: (2006)

Trans-Allelic Model for Prediction of Peptide:MHC-II Interactions
por: Degoot, Abdoelnaser M., et al.
Publicado: (2018)

Functional recombinant MHC class II molecules and high-throughput peptide-binding assays
por: Justesen, Sune, et al.
Publicado: (2009)

Prediction of peptides binding to MHC class I and II alleles by temporal motif mining
por: Meydan, Cem, et al.
Publicado: (2013)

MHC class II complexes sample intermediate states along the peptide exchange pathway
por: Wieczorek, Marek, et al.
Publicado: (2016)

MHC class II-derived peptides can bind to class II molecules, including self molecules, and prevent antigen presentation
Publicado: (1990)

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

The MHC class I peptide repertoire is molded by the transcriptome
por: Fortier, Marie-Hélène, et al.
Publicado: (2008)

MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes
por: Bordner, Andrew J, et al.
Publicado: (2010)

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)

Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation
por: Wieczorek, Marek, et al.
Publicado: (2017)

Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms
por: Rajapakse, Menaka, et al.
Publicado: (2007)

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

Transition of tumor-associated macrophages from MHC class II(hi )to MHC class II(low )mediates tumor progression in mice
por: Wang, Benfan, et al.
Publicado: (2011)

PML promotes MHC class II gene expression by stabilizing the class II transactivator
por: Ulbricht, Tobias, et al.
Publicado: (2012)

Drug activity prediction using multiple-instance learning via joint instance and feature selection
por: Zhao, Zhendong, et al.
Publicado: (2013)

Multiple instance learning of Calmodulin binding sites
por: Minhas, Fayyaz ul Amir Afsar, et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_936o5j2ri39ln3cflqi7uueuvn