Table 3.
Antibody docking methods.
| Tools | Docking mode | URL | Algorithm | References |
|---|---|---|---|---|
| ClusPro | Have Ab specific mode | https://cluspro.bu.edu/login.php | FFT based | [99] |
| SnugDock/Rosseta | Have Ab specific mode | https://rosie.graylab.jhu.edu/snug_dock | Semi flexible docking with energy minimization | [49], [102], [123] |
| FRODOCK2.0 | Have Ab specific mode | http://frodock.chaconlab.org/ | FFT based | [101] |
| PatchDock/ FireDock | Have Ab specific mode | https://bioinfo3d.cs.tau.ac.il/PatchDock/, http://bioinfo3d.cs.tau.ac.il/FireDock/ | Geometric hashing based | [100], [124] |
| HADDOCK2.2 | Not Ab specific mode | https://haddock.science.uu.nl/services/HADDOCK2.2/ | MC simulated annealing based | [103] |
| ZDOCK | Not Ab specific mode | http://zdock.umassmed.edu/ | FFT based | [105] |
| SwarmDock | Not Ab specific mode | https://bmm.crick.ac.uk/~svc-bmm-swarmdock/ | Flexible docking with Particle Swarm Optimization (PSO) | [125] |
| LightDock | Not Ab specific mode | https://lightdock.org/ | Flexible docking with Glowworm Swarm Optimization (GSO) | [104] |
| pyDockWeb/ pyDock | Not Ab specific mode | https://life.bsc.es/pid/pydockweb | FFT based | [126] |
| HDOCK | Not Ab specific mode | http://hdock.phys.hust.edu.cn/ | FFT based | [127] |
| HexServer | Not Ab specific mode | http://hexserver.loria.fr/ | FFT based | [128] |
| ATTRACT | Not Ab specific mode | http://www.attract.ph.tum.de/services/ATTRACT/ | Energy minimization | [129] |
| GRAMM-X | Not Ab specific mode | http://vakser.compbio.ku.edu/resources/gramm/grammx/ | FFT based | [130] |