EpiJen: a server for multistep T cell epitope prediction (Q33236277)

24 July 2017

title

EpiJen: a server for multistep T cell epitope prediction (English)

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24 July 2017

Irini A Doytchinova

1

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author name string

Pingping Guan

series ordinal

2

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24 July 2017

Darren R Flower

series ordinal

3

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24 July 2017

publication date

13 March 2006

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24 July 2017

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24 July 2017

volume

7

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24 July 2017

page(s)

131

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AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data

24 July 2017

cites work

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Integrated modeling of the major events in the MHC class I antigen processing pathway

14 July 2018

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Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method

14 July 2018

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Unanticipated antigens: translation initiation at CUG with leucine

14 July 2018

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An antigenic peptide produced by peptide splicing in the proteasome

14 July 2018

1 reference

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Immune recognition of a human renal cancer antigen through post-translational protein splicing.

14 July 2018

1 reference

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Towards in silico prediction of immunogenic epitopes

14 July 2018

1 reference

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Quantitative online prediction of peptide binding to the major histocompatibility complex

14 July 2018

1 reference

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Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors.

14 July 2018

1 reference

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TAP-independent antigen presentation on MHC class I molecules: lessons from Epstein–Barr virus

14 July 2018

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Optimizing vaccine design for cellular processing, MHC binding and TCR recognition

14 July 2018

1 reference

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The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues

14 July 2018

1 reference

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An IFN-gamma-induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I-presented peptides

14 July 2018

1 reference

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ERAAP customizes peptides for MHC class I molecules in the endoplasmic reticulum

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Prediction of MHC class I binding peptides, using SVMHC

14 July 2018

1 reference

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The importance of the proteasome and subsequent proteolytic steps in the generation of antigenic peptides.

14 July 2018

1 reference

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Combining computer algorithms with experimental approaches permits the rapid and accurate identification of T cell epitopes from defined antigens

14 July 2018

1 reference

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A neural network model approach to the study of human TAP transporter

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Differences in the expression of human class I MHC alleles and their associated peptides in the presence of proteasome inhibitors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Differential processing of class-I-restricted epitopes by the standard proteasome and the immunoproteasome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Neural network method for predicting peptides that bind major histocompatibility complex molecules

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Two new proteases in the MHC class I processing pathway

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

An algorithm for the prediction of proteasomal cleavages

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

SYFPEITHI: database for MHC ligands and peptide motifs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Specific proteolytic cleavages limit the diversity of the pool of peptides available to MHC class I molecules in living cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

A giant protease with potential to substitute for some functions of the proteasome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Interferon-gamma can stimulate post-proteasomal trimming of the N terminus of an antigenic peptide by inducing leucine aminopeptidase

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Proteasomes can either generate or destroy MHC class I epitopes: evidence for nonproteasomal epitope generation in the cytosol

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

The generation of MHC class I-associated peptides is only partially inhibited by proteasome inhibitors: involvement of nonproteasomal cytosolic proteases in antigen processing?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Peptide transporter (TAP-1 and TAP-2)-independent endogenous processing of Epstein-Barr virus (EBV) latent membrane protein 2A: implications for cytotoxic T-lymphocyte control of EBV-associated malignancies.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Statistical comparison of established T-cell epitope predictors against a large database of human and murine antigens.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Peptide-dependent expression of HLA-B7 on antigen processing-deficient T2 cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Peptide length and sequence specificity of the mouse TAP1/TAP2 translocator

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Nucleotide binding to the hydrophilic C-terminal domain of the transporter associated with antigen processing (TAP).

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Peptide selection by MHC-encoded TAP transporters

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Functional expression and purification of the ABC transporter complex associated with antigen processing (TAP) in insect cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

MHC ligands and peptide motifs: first listing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Requirements for peptide binding to the human transporter associated with antigen processing revealed by peptide scans and complex peptide libraries

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Ranking potential binding peptides to MHC molecules by a computational threading approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

T cell recognition of an HLA-A2-restricted epitope derived from a cleaved signal sequence

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

A sequence pattern common to T cell epitopes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

T-cell antigenic sites tend to be amphipathic structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Transport protein genes in the murine MHC: possible implications for antigen processing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

HLA-A2.1-associated peptides from a mutant cell line: a second pathway of antigen presentation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

MHCPred 2.0: an updated quantitative T-cell epitope prediction server.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Class I T-cell epitope prediction: improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Translation from cryptic reading frames of DNA vaccines generates an extended repertoire of immunogenic, MHC class I-restricted epitopes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Coupling in silico and in vitro analysis of peptide-MHC binding: a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

MAPPP: MHC class I antigenic peptide processing prediction.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Analysis and prediction of affinity of TAP binding peptides using cascade SVM.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Application of support vector machines for T-cell epitopes prediction

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

A MATHEMATICAL CONTRIBUTION TO STRUCTURE-ACTIVITY STUDIES.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

The HLA-A2-supermotif: a QSAR definition.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Prediction of MHC class I binding peptides using profile motifs.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Prediction of proteasome cleavage motifs by neural networks

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Distinct proteolytic processes generate the C and N termini of MHC class I-binding peptides.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Neural network-based prediction of candidate T-cell epitopes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

The MHC class I ligand-generating system: roles of immunoproteasomes and the interferon-gamma-inducible proteasome activator PA28.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Evidence for the presence of five distinct proteolytic components in the pituitary multicatalytic proteinase complex. Properties of two components cleaving bonds on the carboxyl side of branched chain and small neutral amino acids

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Using a neural network to identify potential HLA-DR1 binding sites within proteins.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1421443

Prediction of peptide affinity to HLA DRB1*0401

31 October 2018

1 reference

12 December 2020

HLA-A3 supermotif defined by quantitative structure-activity relationship analysis

1 reference

12 December 2020

Human peptide transporter deficiency: importance of HLA-B in the presentation of TAP-independent EBV antigens

1 reference

12 December 2020

Transporter Associated with Antigen Processing Preselection of Peptides Binding to the MHC: A Bioinformatic Evaluation

1 reference

12 December 2020

Use of serine-protease inhibitors as probes for the different proteolytic activities of the rat liver multicatalytic proteinase complex

1 reference

12 December 2020

Toward the Quantitative Prediction of T-Cell Epitopes: CoMFA and CoMSIA Studies of Peptides with Affinity for the Class I MHC Molecule HLA-A*0201

1 reference

12 December 2020

A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif

1 reference

12 December 2020

Pituitary multicatalytic proteinase complex. Specificity of components and aspects of proteolytic activity

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-7-131

1 reference

journals/bmcbi/DoytchinovaGF06

24 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

24 July 2017

1 reference