Tag: epitope

epitope3D – Machine Learning method for conformational B-cell Epitope prediction

epitope3D

:: DESCRIPTION

epitope3D is a novel scalable machine learning method capable of accurately identifying conformational epitopes trained and evaluated on the largest curated epitope data set to date.

::DEVELOPER

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

da Silva BM, Myung Y, Ascher DB, Pires DEV.
epitope3D: a machine learning method for conformational B-cell epitope prediction.
Brief Bioinform. 2021 Oct 21:bbab423. doi: 10.1093/bib/bbab423. Epub ahead of print. PMID: 34676398.

SEPPA 3.0 – Server for Conformational B-cell Epitope Prediction

SEPPA 3.0

:: DESCRIPTION

SEPPA (Spatial Epitope Prediction of Protein Antigens) is spatial epitope prediction for protein antigens, particularly for N-linked glycoproteinsmeu ip

::DEVELOPER

Dr. Zhiwei Cao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Winodows / Linux
  • Python
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhou C, Chen Z, Zhang L, Yan D, Mao T, Tang K, Qiu T, Cao Z.
SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens.
Nucleic Acids Res. 2019 Jul 2;47(W1):W388-W394. doi: 10.1093/nar/gkz413. PMID: 31114919; PMCID: PMC6602482.
SEPPA 2.0-more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen.
Qi T, Qiu T, Zhang Q, Tang K, Fan Y, Qiu J, Wu D, Zhang W, Chen Y, Gao J, Zhu R, Cao Z.
Nucleic Acids Res. 2014 May 16. pii: gku395

PEASE – Predicting Epitopes using Antibody Sequence

PEASE

:: DESCRIPTION

PEASE is an automated tool for predicting the epitope for a given antigen structure and an antibody sequence.

::DEVELOPER

Yanay Ofran’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PEASE: Predicting B-Cell Epitopes utilizing Antibody Sequence.
Sela-Culang I, Ashkenazi S, Peters B, Ofran Y.
Bioinformatics. 2014 Nov 27. pii: btu790

EpIC – Epitope Immunogenicity Characterization

EpIC

:: DESCRIPTION

EpIC is a software program that is designed to enable optimization of peptide epitopes for vaccine applications. Peptide-based vaccines offer many advantages over traditional vaccine platforms in terms of cost, safety, and ease of production.

::DEVELOPER

Bioinformatics Research Group, University of Saskatchewan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

EpIC: A Rational Pipeline for Epitope Immunogenicity Characterization.
Marciniuk K, Trost B, Napper S.
Bioinformatics. 2015 Mar 6. pii: btv136

ProInflam – Prediction of Proinflamatory Epitopes

ProInflam

:: DESCRIPTION

ProInflam is a webserver for the prediction of proinflammatory antigenicity of peptides and proteins.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins.
Gupta S, Madhu MK, Sharma AK, Sharma VK.
J Transl Med. 2016 Jun 14;14(1):178. doi: 10.1186/s12967-016-0928-3.

EPISOFT – Epitope Vaccine Optimization Server

EPISOFT

:: DESCRIPTION

EPISOFT predicts epitope HLA I binding profiles and computes population protection (PPC). It also identifies minimal sets of epitopes that reach a target PPC for 5 distinct user-selected ethnic groups.

::DEVELOPER

Immunomedicine Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

Towards the Knowledge-based Design of Universal Influenza Epitope Ensemble Vaccines.
Sheikh QM, Gatherer D, Reche PA, Flower DR.
Bioinformatics. 2016 Jul 10. pii: btw399.

TepiTool – Computational Prediction of T Cell Epitope Candidates

TepiTool

:: DESCRIPTION

The Tepitool provides prediction of peptides binding to MHC class I and class II molecules.

::DEVELOPER

the IEDB Solutions Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TepiTool

:: MORE INFORMATION

Citation

TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates.
Paul S, Sidney J, Sette A, Peters B.
Curr Protoc Immunol. 2016 Aug 1;114:18.19.1-18.19.24. doi: 10.1002/cpim.12.

EPITOPEFINDER 0.11 – Finding Immune Epitopes

EPITOPEFINDER 0.11

:: DESCRIPTION

epitopefinder is a Python package for analyzing immune epitopes in a protein, where the epitopes are mined from the Immune Epitope Database.

::DEVELOPER

Bloom Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 EPITOPEFINDER

:: MORE INFORMATION

Citation

L. Ian Gong and Jesse D. Bloom.
“Epistatically interacting substitutions are enriched during adaptive protein evolution.”
PLoS Genetics. 10:e1004328 (2014)

BepiPred 2.0c – Linear B-cell epitopes

BepiPred 2.0c

:: DESCRIPTION

BepiPred predicts the location of linear B-cell epitopes using a combination of a hidden Markov model and a propensity scale method.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BepiPred

:: MORE INFORMATION

Citation

Improved method for predicting linear B-cell epitopes
Jens Erik Pontoppidan Larsen, Ole Lund and Morten Nielsen
Immunome Research 2:2, 2006.