Table 1.
Summary of currently available resources for computational/structural annotation of antibody sequences.
| Tool type | Tool name and reference | Short tool description |
|---|---|---|
| ANTIBODY NUMBERING | ANARCI (113) | Variety of schemes (North, Chothia, Kabat, IMGT, AHo). Both online and command line versions are available |
| ANTIBODY NUMBERING | Abnum (71) | Online numbering tool that operates with Kabat and Chothia schemes |
| SEQUENCE ANALYSIS | IgBLAST (114) | Nucleotide and amino-acid antibody sequence analysis in IMGT and KABAT schemes |
| SEQUENCE ANALYSIS | IMGT/HighV-QUEST (115) | Online antibody nucleotide sequence analysis in IMGT numbering scheme |
| STRUCTURE DATABASE | SabDab (29) | Weekly updating database of all publically available antibody structures. |
| STRUCTURE/SEQUENCE DATABASE | abYsis (116) | Database of antibody structures and sequences |
| SEQUENCE DATABASE | DIGIT (111) | Database of antibody sequences |
| ANTIBODY MODELING | ABodyBuilder (8) | Homology modeling (30 s per model) |
| ANTIBODY MODELING | PIGSPro (86) | Homology modeling |
| ANTIBODY MODELING | Kotai Antibody Builder (95) | Homology modeling (90 min per model) |
| ANTIBODY MODELING | Accelrys (101) | Hybrid modeling (30 min per model) |
| ANTIBODY MODELING | RosettaAntibody (87) | Ab initio modeling (482 CPU hours per model) |
| ANTIBODY MODELING (COMMERCIAL) | Chemical Computing group (80) | Homology modeling tool combined with molecular dynamics (30 min per model) |
| CDR-H3 MODELING | Sphinx (102) | Length-independent hybrid modeling (30 min per model) |
| CDR-H3 MODELING | PLOP (99) | Ab initio modeling |
| CDR-H3 MODELING | FREAD (85) | Homology modeling (2 min per model) |
| PARATOPE PREDICTION | Paratome (117) | Structural consensus to identify additional antigen recognizing regions outside the CDRs |
| PARATOPE PREDICTION | i-Patch (118) | Statistical inference to devise a likelihood for a position to form a potential contact |
| PARATOPE PREDICTION | proABC (119) | Sequence-based method that leverages machine learning to predict residues that form interactions |
Many of these tools have online presence and links to these are available on our website http://antibodystructure.org.