Structural Antibody Tools.

Here we compile the list of computational tools you can use to annotate and structurally model antibody sequences. Scroll down the page to browse the tools.

If you find this information useful and you would like to cite it, please refer to:

How B-cell receptor repertoire sequencing can be enriched with structural antibody data. Kovaltsuk, A. Krawczyk K et al. Frontiers in Immunology,

Tools

Please click on the name of the tool to go to its webpage.

Tool TypeTool nameTool Description
Antibody NumberingANARCIOnline and offline numbering of antibodies using variety of schemes (North, Chothia, Kabat, IMGT etc.s)
Antibody NumberingAbnumOnline numbering of antibodies.
Sequence AnalysisIgBLASTNucleotide and amino acid antibody sequence analysis in IMGT and KABAT schemes.
Sequence AnalysisIMGT/V-QUESTOnline antibody nucleotide sequence analysis in IMGT numbering scheme.
Structure DatabaseSAbDabSelf-updateable database of antibody structures.
Structure/Sequence DatabaseAbysisDatabase of antibody structures and sequences.
Sequence DatabaseDIGITDatabase of antibody sequences
Fv ModelingABodyBuilderVery rapid modeling of the entire antibody Fv region (0.5 m per model)
Fv ModelingPIGSProRapid modeling of entire Fv region.
Fv ModelingKotai Antibody BuilderRapid modeling of entire Fv region. (90m per model)
Fv ModelingRosettaAntibodyModeling of entire Fv region (up to several days)
Fv ModelingAccelrysHybrid modeling (30m per model)
Protein ModelingMODELLERGeneral-purpose protein modeling software.
Loop ModelingSphinxH3-specific loop modeling.
Loop ModelingFREADGeneric template-based loop modeling software.
Loop ModelingPLOPAb initio loop modeling software.
Paratope PredictionParatomeStructural consensus to identify additional antigen recognizing regions outside the CDRs
Paratope PredictionAntibody i-PatchStatistical inference to devise a likelihood for a position to form a potential contact
Paratope PredictionproABCSequence-based method that leverages machine learning to predict residues that form interactions