Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification (Q36260214)

13 August 2017

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification (English)

1 reference

13 August 2017

Morten Nielsen

6

0 references

Anette Stryhn

4

object named as

Anette Stryhn

1 reference

13 August 2017

Massimo Andreatta

1

1 reference

13 August 2017

Edita Karosiene

2

1 reference

13 August 2017

Michael Rasmussen

3

1 reference

13 August 2017

Søren Buus

5

1 reference

13 August 2017

language of work or name

English

0 references

publication date

29 September 2015

1 reference

13 August 2017

1 reference

13 August 2017

67

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13 August 2017

11-12

1 reference

13 August 2017

641-650

1 reference

https://scigraph.springernature.com/pub.10.1007/s00251-015-0873-y

13 August 2017

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cites work

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Frequency Patterns of T-Cell Exposed Amino Acid Motifs in Immunoglobulin Heavy Chain Peptides Presented by MHCs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

The immune epitope database (IEDB) 3.0.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

MHC class II tetramers made from isolated recombinant α and β chains refolded with affinity-tagged peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Heterologous immunity between viruses

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

SVRMHC prediction server for MHC-binding peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

How TCRs bind MHCs, peptides, and coreceptors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Specificity and degeneracy of T cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Cutting edge: TCR contacts as anchors: effects on affinity and HLA-DM stability

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

A functional and structural basis for TCR cross-reactivity in multiple sclerosis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Autoimmunity provoked by infection: how good is the case for T cell epitope mimicry?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Naturally processed HLA class II peptides reveal highly conserved immunogenic flanking region sequence preferences that reflect antigen processing rather than peptide-MHC interactions.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Molecular basis for recognition of an arthritic peptide and a foreign epitope on distinct MHC molecules by a single TCR.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Specificity and promiscuity among naturally processed peptides bound to HLA-DR alleles

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

MHC-dependent antigen processing and peptide presentation: providing ligands for T lymphocyte activation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Amino acid substitution matrices from protein blocks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

The majority of immunogenic epitopes generate CD4+ T cells that are dependent on MHC class II-bound peptide-flanking residues

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Antigen presentation by MHC class II molecules: invariant chain function, protein trafficking, and the molecular basis of diverse determinant capture

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Why must T cells be cross-reactive?

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Characterizing the binding motifs of 11 common human HLA-DP and HLA-DQ molecules using NNAlign.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Functional recombinant MHC class II molecules and high-throughput peptide-binding assays

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4637192

22 September 2018

Neural network ensembles

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS00251-015-0873-Y

Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS00251-015-0873-Y

Capacity of intact proteins to bind to MHC class II molecules

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26416257

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

T cell receptor recognition of MHC class II-bound peptide flanking residues enhances immunogenicity and results in altered TCR V region usage

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26416257

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Computer-assisted prediction of HLA-DR binding and experimental analysis for human promiscuous Th1-cell peptides in the 24 kDa secreted lipoprotein (LppX) of Mycobacterium tuberculosis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26416257

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S00251-015-0873-Y

1 reference

13 August 2017

1 reference

13 August 2017

1 reference