Antibody Tools

Download antibody software developed by OPIG

Please cite the corresponding publication

ABodyBuilder is an automated antibody Fv/nanobody modelling tool. It predicts the orientation based on the ABangle parameters, the CDR loops via FREAD, and the side chains are modelling using SCWRL. In cases where the loops cannot be predicted by FREAD, and/or clashes are found in the model, MODELLER is used to resolve these issues.

For a full description of the pipeline, or if you use this software, please refer to:
Leem J, et al. ABodyBuilder: automated antibody structure prediction with data-driven accuracy estimation. mAbs. (2016)

We have developed a decoy re-scoring method which uses antibody-specific statistics to identify better decoys. Using our re-scoring scheme you can re-order the decoys obtained from ZDOCK to enrich the top ten results with more native antibody-antigen poses generated by the docking software. The re-scoring correctly identifies more native antibody-antigen decoys even if a homology model is supplied as the antibody structure.

For a full description of the method or if you use this software, please refer to:

Krawczyk et al. Antibody i-Patch prediction of the antibody binding site improves rigid local antibody–antigen docking. PEDS (2013)

We have developed a CDR contact prediction method, Antibody i-Patch, which uses antibody-specific statistics. The software annotates CDR residues with a score indicating the likelihood of the given residue to be in contact with the supplied antigen. Antibody i-Patch works well with only the homology model of the antibody supplied as input.

For a full description of the method or if you use this software, please refer to:

Krawczyk et al. Antibody i-Patch prediction of the antibody binding site improves rigid local antibody–antigen docking. PEDS (2013)

We have developed a method and tool, ABangle, to calculate and analyse the orientation between the antibody variable domains, VH and VL.

For a full description of the method or if you use this software, please refer to:

Dunbar et al. ABangle: characterising the VH–VL orientation in antibodies. PEDS (2013)

We have developed a tool, ANARCI, to apply commonly used numbering schemes to antibody and TCR variable domain sequences.

For a full description of the method or if you use this software, please refer to:

Dunbar et al. ANARCI: Antigen receptor numbering and receptor classification. Bioinformatics (2016) 32(2) 298-300