Paratome 1.0 – Identification of Antigen Binding Regions

Paratome 1.0

:: DESCRIPTION

Paratome is an automated tool for the identification of Antigen Binding Regions (ABRs).

::DEVELOPER

Yanay Ofran’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Paratome

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W521-4. doi: 10.1093/nar/gks480. Epub 2012 Jun 6.
Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure.
Kunik V1, Ashkenazi S, Ofran Y.

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

 NO

:: 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.

Antigen Explorer – Antigen Combinations for Precision Cancer Recognition

Antigen Explorer

:: DESCRIPTION

Antigen Explorer is an interactive resource for browsing antigen combinations for more precise tumor recognition. Leveraging expression data from TCGA and GTEx, the discrimination potential of all possible combinations of surface antigens were scored for 33 tumor types. Users can explore the top predictions and make interactive plots to evaluate an antigen pair against normal tissue cross-reactivity.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Dannenfelser R, Allen GM, VanderSluis B, Koegel AK, Levinson S, Stark SR, Yao V, Tadych A, Troyanskaya OG, Lim WA.
Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies.
Cell Syst. 2020 Sep 23;11(3):215-228.e5. doi: 10.1016/j.cels.2020.08.002. Epub 2020 Sep 10. PMID: 32916097; PMCID: PMC7814417.

BASELINe 1.3 – Bayesian Estimation of Antigen-Driven Selection in Immunoglobulin Sequences

BASELINe 1.3

:: DESCRIPTION

BASELINe, a new computational framework for Bayesian estimation of Antigen-driven selection in Immunoglobulin sequences, provides a more intuitive means of analyzing selection by actually quantifying it.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 BASELINe

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep 1;40(17):e134. Epub 2012 May 27.
Quantifying selection in high-throughput Immunoglobulin sequencing data sets.
Yaari G1, Uduman M, Kleinstein SH.

ANARCI – Antigen Receptor Numbering And Receptor ClassificatIon

ANARCI

:: DESCRIPTION

ANARCI is a tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 ANARCI

:: MORE INFORMATION

Citation:

ANARCI: Antigen receptor numbering and receptor classification.
Dunbar J, Deane CM.
Bioinformatics. 2015 Sep 30. pii: btv552.

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

  NO

:: 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

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