Tag: B-cell

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

Mimox 2 – Comformational B-cell Eitope Prediction tool

Mimox 2

:: DESCRIPTION

Mimox is an auto comformational B-cell eitope prediction tool,which is designed to find out the B-cell epitope on the input antigen structure with the information of mimotope sequences from the corresponding phage display experiment.

::DEVELOPER

HLAB: Huang’s LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MIMOX: a web tool for phage display based epitope mapping.
Huang J, Gutteridge A, Honda W, Kanehisa M.
BMC Bioinformatics. 2006 Oct 12;7:451.

ARResT / AssignSubsets 20191110 – Robust Subclassification of Chronic Lymphocytic Leukemia based on B cell Receptor IG stereotypy

ARResT / AssignSubsets 20191110

:: DESCRIPTION

ARResT is designed to enable a deep understanding of antigen receptor sequences with a cascade of algorithms and databases.

ARResT/AssignSubsets was built to robustly assign user-submitted sequences as new members to existing subsets of stereotyped antigen receptor sequences, currently applicable to the 19 major subsets of stereotyped B-cell receptors in chronic lymphocytic leukemia (CLL), through sets of rules captured in a statistical model.

::DEVELOPER

The Bioinformatics Analysis Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy.
Bystry V, Agathangelidis A, Bikos V, Sutton LA, Baliakas P, Hadzidimitriou A, Stamatopoulos K, Darzentas N.
Bioinformatics. 2015 Aug 6. pii: btv456.

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.

EpiPred – B-cell Epitope Prediction

EpiPred

:: DESCRIPTION

EpiPred is a software of B-cell epitope prediction and antibody-antigen docking

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE
  • Python

:: DOWNLOAD

 EpiPred

:: MORE INFORMATION

Citation:

Improving B-cell epitope prediction and its application to global antibody-antigen docking.
Krawczyk K, Liu X, Baker T, Shi J, Deane CM.
Bioinformatics. 2014 Aug 15;30(16):2288-94. doi: 10.1093/bioinformatics/btu190.

ABCpred – Artificial Neural Network based B-cell Epitope Prediction Server

ABCpred

:: DESCRIPTION

ABCpred server is to predict linear B cell epitope regions in an antigen sequence, using artificial neural network. This server will assist in locating epitope regions that are useful in selecting synthetic vaccine candidates, disease diagonosis and also in allergy research.

::DEVELOPER

ABCpred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Saha, S and Raghava G.P.S. (2006)
Prediction of Continuous B-cell Epitopes in an Antigen Using Recurrent Neural Network.
Proteins,65(1),40-48

BcePred – Predict B cell Epitope based on Physio-chemical Properties of Amino Acids

BcePred

:: DESCRIPTION

The BcePred server predicts B cell epitope based on physio-chemical properties of amino acids.

::DEVELOPER

BcePred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Saha.S and Raghava G.P.S.
BcePred:Prediction of Continuous B-Cell Epitopes in Antigenic Sequences Using Physico-chemical Properties.
In G.Nicosia, V.Cutello, P.J. Bentley and J.Timis (Eds.) ICARIS 2004, LNCS 3239, 197-204, Springer,2004.