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Links tagged with 'epitopes'

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AlgPredTool Content

http://www.imtech.res.in/raghava/algpred/ [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.

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links directory index: 57
TitlePublication YearGoogle Scholar Citation Count
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes200657
NAR Web Server Issue 2006
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tagsalgorithms allergens amino acid motifs amino acids artificial intelligence epitope mapping epitopes immunoglobulin e proteins

AntigenDBDatabase Content

http://www.imtech.res.in/raghava/antigendb/ [open in a new window]

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Human Genome > Databases

AntigenDB contains 500 antigens to pathogenic species curated from the literature and other immunological resources. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases.

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links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
AntigenDB: an immunoinformatics database of pathogen antigens201010
NAR Database Issue 2010
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tagsantigens communicable diseases computational biology epitopes genetic databases humans immune system immunogenetics lymphocytes peptide mapping post-translational protein processing protein databases tertiary protein structure

CTLPredTool Content

http://www.imtech.res.in/raghava/ctlpred [open in a new window]

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Protein > 3-D Structure Comparison
Protein > Domains and Motifs

CTLPred is a direct method for prediction of CTL epitopes crucial in subunit vaccine design.In direct methods the information or patterns of T cell epitopes instead of MHC binders were used for the development of methods.

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links directory index: 100
TitlePublication YearGoogle Scholar Citation Count
Prediction of CTL epitopes using QM, SVM and ANN techniques2004100
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tagsalgorithms ANN antigens artificial intelligence cytotoxic T lymphocyte cytotoxic t-lymphocytes epitopes genetic databases humans major histocompatibility complex neural networks (computer) predictive value of tests QM SVM

IEDB-3DDatabase Content

http://www.iedb.org [open in a new window]

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Protein > Databases

IEDB-3D is the 3D structural component of the Immune Epitope Database (IEDB). IEDB-3D catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB). Journal articles that are primary citations of PDB structures and that define immune epitopes are curated within IEDB along with accompanying functional assays and immunologically relevant information. For each curated structure, IEDB-3D provides calculated data on intermolecular contacts and interface areas and includes an application, EpitopeViewer, to visualize the structures. IEDB-3D is fully embedded within IEDB, thus allowing structural data, both curated and calculated, and all accompanying information to be queried using multiple search interfaces. These include queries for epitopes recognized in different pathogens, eliciting different functional immune responses, and recognized by different components of the immune system.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
IEDB-3D: structural data within the immune epitope database20113
NAR Database Issue 2011
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tagsantibodies antigen receptors b-lymphocyte epitopes epitopes histocompatibility antigens ligands protein conformation protein databases t-lymphocyte epitopes

Immune Epitope DatabaseDatabase Content

http://tools.immuneepitope.org/ [open in a new window]

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Human Genome > Databases
Protein > Databases

The Immune Epitope Database (IEDB) provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes. Epitopes recognized in humans, nonhuman primates, rodents, pigs, cats and all other tested species are included. Both positive and negative experimental results are captured. The database can be queried by epitope structure, source organism, MHC restriction, assay type or host organism, among other criteria.

links directory index: 109
TitlePublication YearGoogle Scholar Citation Count
The immune epitope database 2.02010109
NAR Database Issue 2010
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tagsanimals communicable diseases computational biology epitopes genetic databases humans immune system immunogenetics major histocompatibility complex peptides protein databases proteins

NetMHC-3.0Tool Content

http://www.cbs.dtu.dk/services/NetMHC [open in a new window]

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Human Genome > Health and Disease
Protein > Molecular Dynamics and Docking

NetNHC-3.0 is a web server for the prediction of human, mouse or monkey MHC Class I-peptide binding. Predictions are made for peptides of 8-11 amino acid length using artificial neural networks and weight matrices.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11200864
NAR Web Server Issue 2008
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tagsalleles animals epitopes haplorhini histocompatibility antigens class i hla antigens humans mice peptides

nHLAPredTool Content

http://www.imtech.res.in/raghava/nhlapred [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Domains and Motifs

A highly accurate method for predicting MHC Class I restricted T cell epitopes for a large number of MHC Class I alleles.

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links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes200735
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tagsalleles animals computational biology epitopes genetic databases histocompatibility antigens class i humans MHC class I mhc class i genes neural networks (computer) peptides prediction proteasome endopeptidase complex T cell t-lymphocyte epitopes

ReMusTool Content

http://140.121.196.30/remus.asp [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Features

REinforced Merging techniques for Unique peptide Segments (ReMus) is designed for identification of the locations and compositions of unique peptide segments from a set of protein family sequences.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
Unique peptide identification of RNase A superfamily sequences based on reinforced merging algorithms20063
REMUS: a tool for identification of unique peptide segments as epitopes200611
A reinforced merging methodology for mapping unique peptide motifs in members of protein families20068
NAR Web Server Issue 2006
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals antibody specificity cattle chemical models computational biology conserved sequence epitope mapping epitopes humans mice molecular models molecular sequence data monoclonal antibodies pancreatic ribonuclease peptides protein conformation protein sequence analysis proteins sequence alignment structure-activity relationship

SEPPATool Content

http://lifecenter.sgst.cn/seppa/index.php [open in a new window]

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Protein > 3-D Structure Prediction

A computational server for Spatial Epitope Prediction of Protein Antigens (SEPPA) based on a 'unit patch of residue triangle' description of local spatial context in protein surface.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
SEPPA: a computational server for spatial epitope prediction of protein antigens200919
NAR Web Server Issue 2009
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tagscomputational biology epitope mapping epitopes proteins reproducibility of results

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