Selected open-source tools that have been used for ultra-large VS and their associated repositories. Screening library type describes what kind of screening library or space the tool uses: enumerated (libraries), reagent space (e.g., fragment-based, synthon-based), or non-enumerated (spaces).
N. B. This list is not exhaustive.
Last checked and updated 2025-02-21
| Tool | Repository | Reference(s) | Screening library type |
|---|---|---|---|
| Conformal Predictor | GitHub Carlssonlab/conformalpredictor | Luttens et al. (2023) Preprint. DOI 10.26434/chemrxiv-2023-w3x36 | enumerated |
| DeepDocking | GitHub jamesgleave/DD_protocol | Gentile et al. (2020) ACS Cent Sci 6(6): 939-949. DOI 10.1021/acscentsci.0c00229 | enumerated |
| DeepDocking GUI | GitHub jamesgleave/DeepDockingGUI | Yaacoub et al. (2022) Bioinformatics 38(4): 1146-1148. DOI 10.1093/bioinformatics/btab771 | enumerated |
| HASTEN | GitHub TuomoKalliokoski/HASTEN | Kalliokoski (2021) Mol Inform 40(9): 2100089. DOI 10.1002/minf.202100089 | enumerated |
| KarmaDock | GitHub schrojunzhang/KarmaDock | Zhang et al. (2023) Nat Comput Sci 3: 789-804. DOI 10.1038/s43588-023-00511-5 | enumerated |
| Lean docking Encoder | GitHub UnixJunkie/molenc | Berenger et al. (2021) J Chem Inf Model 61(5): 2341-2352. DOI 10.1021/acs.jcim.0c01452 | enumerated |
| Lean docking Support Vector Regressor | GitHub UnixJunkie/linwrap | Berenger et al. (2021) J Chem Inf Model 61(5): 2341-2352. DOI 10.1021/acs.jcim.0c01452 | enumerated |
| Linear accelerated docking | GitHub marinegor/Linear-accelerated-docking | Marin et al. (2024) J Chem Inf Model 64(7): 2612-2623. DOI 10.1021/acs.jcim.3c01661 | enumerated |
| MolPAL | GitHub coleygroup/molpal | Graff et al. (2021) Chem Sci 12(22): 7866-7881. DOI 10.1039/d0sc06805e | enumerated |
| OpenVS | GitHub gfzhou/OpenVS | Zhou et al. (2024) Nat Commun 15: 7761. DOI 10.1038/s41467-024-52061-7 | enumerated |
| PharmacoNet | GitHub SeonghwanSeo/PharmacoNet | Seo & Kim (2024) Chem Sci 15: 19473-19487. DOI 10.1039/D4SC04854G | enumerated |
| Schrödinger GPU Similarity (incentive) | GitHub schrodinger/gpusimilarity | enumerated | |
| SpaceDock | GitHub litfsindt/LIT-SpaceDock | Sindt et al. (2024) ACS Cent Sci 10(3): 615–627. DOI 10.1021/acscentsci.3c01521 | reagent space |
| SpaceGA | GitHub lmoesgaard/SpaceGA | Moesgaard & Kongsted (2024) J Chem Inf Model 64(21): 8123-8130. DOI 10.1021/acs.jcim.4c01308 | non-enumerated (also AL, GA: enumerated) |
| SpaceHASTEN | GitHub TuomoKalliokoski/SpaceHASTEN | Kalliokoski et al. (2025) J Chem Inf Model 65(1): 125-132. DOI 10.1021/acs.jcim.4c01790 | non-enumerated |
| Thompson sampling | GitHub PatWalters/TS | Klarich et al. (2024) J Chem Inf Model 64(4): 1158-1171. DOI 10.1021/acs.jcim.3c01790 | reagent space |
| Uni-Dock | GitHub dptech-corp/Uni-Dock | Yu et al. (2023) J Chem Theory Comput 19(11): 3336-3345. DOI 10.1021/acs.jctc.2c01145 | enumerated |
| V-SYNTHES | GitHub katritchlab/V-SYNTHES | Sadybekov et al. (2022) Nature 601: 452-459. DOI 10.1038/s41586-021-04220-9 | reagent space |
| VirtualFlow | GitHub VirtualFlow | Gorgulla et al. (2020) Nature 580: 663-668. DOI 10.1038/s41586-020-2117-z | enumerated |
| warpDOCK | GitHub BruningLab/warpDOCK | McDougal et al. (2023) ACS Omega 8(32): 29143-29149. DOI 10.1021/acsomega.3c02249 | enumerated |