CSM-AB / mCSM-AB / mCSM-AB2 / mmCSM-AB- Predicting Antibody-antigen Binding Affinity

CSM-AB / mCSM-AB / mCSM-AB2 / mmCSM-AB

:: DESCRIPTION

CSM-AB is a machine learning method capable of predicting antibody-antigen binding affinity by modelling interaction interfaces as graph-based signatures.

mCSM-AB is a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures

mCSM-AB2 is an updated and refined version approach, capable of accurately modelling the effects of mutations on antibody-antigen binding affinity, through the inclusion of evolutionary and energetic terms.

mmCSM-AB is a tool for analysing the effects of introducing multiple point mutations on antibody-antigen binding affinity.

::DEVELOPER

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Myung Y, Pires DEV, Ascher DB.
CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function.
Bioinformatics. 2021 Nov 4:btab762. doi: 10.1093/bioinformatics/btab762. Epub ahead of print. PMID: 34734992.

mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures.
Pires DE, Ascher DB.
Nucleic Acids Res. 2016 May 23. pii: gkw458.

Myung Y, Rodrigues CHM, Ascher DB, Pires DEV.
mCSM-AB2: guiding rational antibody design using graph-based signatures.
Bioinformatics. 2020 Mar 1;36(5):1453-1459. doi: 10.1093/bioinformatics/btz779. PMID: 31665262.

Myung Y, Pires DEV, Ascher DB.
mmCSM-AB: guiding rational antibody engineering through multiple point mutations.
Nucleic Acids Res. 2020 Jul 2;48(W1):W125-W131. doi: 10.1093/nar/gkaa389. PMID: 32432715; PMCID: PMC7319589.

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

:: 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

Y-Tools 3.1.1 – Construction of Antibody Repertoire and Immunoproteogenomics Analysis

Y-Tools 3.1.1

:: DESCRIPTION

Y-Tools are tools for construction of full-length adaptive immune repertoires and immunoinformatics analysis

::DEVELOPER

Algorithmic Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Y-Tools

:: MORE INFORMATION

Citation

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.
Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA.
Bioinformatics. 2015 Jun 15;31(12):i53-i61. doi: 10.1093/bioinformatics/btv238.

BRepertoire – Analysing Antibody Repertoire Data

BRepertoire

:: DESCRIPTION

BRepertoire is a suite of user-friendly web-based software tools for large-scale statistical analyses of antibody repertoire data. It works on data preprocessed by IMGT, and performs statistical and comparative analyses on-the-fly with versatile plotting options.

::DEVELOPER

Fraternali lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Margreitter C, Lu HC, Townsend C, Stewart A, Dunn-Walters DK, Fraternali F.
BRepertoire: a user-friendly web server for analysing antibody repertoire data.
Nucleic Acids Res. 2018 Jul 2;46(W1):W264-W270. doi: 10.1093/nar/gky276. PMID: 29668996; PMCID: PMC6031031.

AbDesigner – Design of Peptide-directed Antibodies

AbDesigner

:: DESCRIPTION

AbDesigner is a tool for analyzing the amino acid sequence of a given protein to identify optimal immunizing peptides for production of antibodies.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

WEb browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies.
Pisitkun T, Hoffert JD, Saeed F, Knepper MA.
Am J Physiol Cell Physiol. 2012 Jan 1;302(1):C154-64. doi: 10.1152/ajpcell.00325.2011.

Cloanalyst 201506 – Analysis of Antibody Somatic Genetics

Cloanalyst 201506

:: DESCRIPTION

Cloanalyst is the software implementation of our most recent suite of statistical methods for the inference of antigen receptor rearrangements and other analyses useful in the study of antibody somatic genetics. Cloanalyst performs a Bayesian analysis of antibody genes to compute posterior probabilities over rearrangement parameters and unmutated ancestral rearrangements, using either single immunoglobulin polynucleotide sequences or sets of clonally related immunoglobulin sequences.

::DEVELOPER

The Center for Computational Immunology

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows
.NET framework

:: DOWNLOAD

Cloanalyst

:: MORE INFORMATION

Repertoire Builder – High-throughput structural modeling for B-cell and T-cell receptors

Repertoire Builder

:: DESCRIPTION

Repertoire Builder (earlier Kotai Antibody Builder) is a method for generating atomic-resolution, three-dimensional models of B cell receptors (BCRs) or T cell receptors (TCRs) from their amino acid sequences.

::DEVELOPER

Department of Genome Informatics; Research Institute for Microbial Diseases; Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Schritt, et al.;
Repertoire Builder: high-throughput structural modeling of B and T cell receptors
Molecular Systems Design & Engineering; 2019

Kotai Antibody Builder: Automated, high-resolution structural modeling of antibodies.
Yamashita K, Ikeda K, Amada K, Liang S, Tsuchiya Y, Nakamura H, Shirai H, Standley DM.
Bioinformatics. 2014 Jul 26. pii: btu510.

SCALOP – Sequence-based antibody CAnonical LOoP structure annotation

SCALOP

:: DESCRIPTION

SCALOP is a sequence-based canonical form predictor for five of the six complementarity-determining regions (H1, H2, L1, L2 and L3) on an antibody.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOs/ Linux

:: DOWNLOAD

SCALOP

:: MORE INFORMATION

Citation

SCALOP: sequence-based antibody canonical loop structure annotation.
Wong WK, Georges G, Ros F, Kelm S, Lewis AP, Taddese B, Leem J, Deane CM.
Bioinformatics. 2019 May 15;35(10):1774-1776. doi: 10.1093/bioinformatics/bty877.

ABangle – VH-VL Orientation Analysis

ABangle

:: DESCRIPTION

ABangle is a tool for calculating and analysing the VH-VL orientation in antibodies.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

ABangle

:: MORE INFORMATION

Citation:

Protein Eng Des Sel. 2013 Oct;26(10):611-20. doi: 10.1093/protein/gzt020. Epub 2013 May 24.
ABangle: characterising the VH-VL orientation in antibodies.
Dunbar J1, Fuchs A, Shi J, Deane CM.

ABAG – Computation of Antibody/Antigen Concentration and Endpoint Titer

ABAG

:: DESCRIPTION

ABAG allows to compute the endpoint titer and concentration of Antibody(Ab) or Antigen(Ag) from ELISA data. It calculate the Ab/Ag concentration, using the graphical method

::DEVELOPER

G P S Raghavaand J. N. Agrewala

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Raghava G. P. S. and Agrewala J. N. (2001)
A Web Based Method for Computing Endpoint Titer and Concentration of Antibody/Antigen.
Biotech Software and Internet Reports 2(5)196-197