Table 1.
Free and commercially available programs, webservers, and source codes for SBDD and LBDD.
| Function | Software/ Webserver Name |
Availability | Website |
|---|---|---|---|
| Comparative modeling | SWISS-MODEL [32] | Free webserver | https://swissmodel.expasy.org/ |
| Structural geometry confirmation | MODELLER [33] | Free standalone program for academic license or commercially available through BIOVIA |
https://salilab.org/modeller/
https://www.3dsbiovia.com/ |
| Robetta [34] | Free webserver | http://new.robetta.org/ | |
| Prime [35] | Commercially available through Schrödinger | https://www.schrodinger.com/prime | |
| I-TASSER [36,37,38,39,40,41] | Free webserver or standalone program for academic license | https://zhanglab.ccmb.med.umich.edu/I-TASSER/ | |
| HHPred [42,43,44] | Free webserver | https://toolkit.tuebingen.mpg.de/tools/hhpred | |
| Structural geometry confirmation | PROCHECK [45] | Free webserver and source code | https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/ |
| Druggability and binding site prediction Druggability and binding site prediction |
ProSA [46] | Free webserver | https://prosa.services.came.sbg.ac.at/prosa.php |
| VERIFY3D [47] | Free webserver | https://servicesn.mbi.ucla.edu/Verify3D/ | |
| ERRAT [48] | Free webserver | https://servicesn.mbi.ucla.edu/ERRAT/ | |
| PockDrug [49] | Free webserver | http://pockdrug.rpbs.univ-paris-diderot.fr/cgi-bin/index.py?page=home | |
| DoGSiteScorer [50] | Free webserver | https://proteins.plus/ | |
| fpocket [51,52] | Free/open source platform | https://github.com/Discngine/fpocket | |
| CASTp [53,54,55] | Free webserver | http://sts.bioe.uic.edu/castp/calculation.html | |
| PocketQuery [56] | Free webserver | http://pocketquery.csb.pitt.edu/ | |
| PASS [57] | Free/open source platform | http://www.ccl.net/cca/software/UNIX/pass/overview.html | |
| SiteMap [58] | Commercially available through Schrödinger | https://www.schrodinger.com/sitemap | |
| Docking, pharmacophore, and virtual screening Docking, pharmacophore, and virtual screening |
ConCavity [59] | Free webserver | https://compbio.cs.princeton.edu/concavity/ |
| PrankWeb [60] | Free webserver | http://prankweb.cz/ | |
| ProFunc [61] | Free webserver | http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/ | |
| AutoDock [62] and AutoDock Vina [63] | Free standalone program | http://autodock.scripps.edu/ | |
| DOCK [64] | Free/open source platform | http://dock.compbio.ucsf.edu/ | |
| GOLD [65] | Commercially available through CCDC | https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/ | |
| Glide [66] | Commercially available through Schrödinger | https://www.schrodinger.com/glide/ | |
| Induced Fit [67] | Commercially available through Schrödinger | https://www.schrodinger.com/induced-fit | |
| FlexX [68] | Commercially available through BioSolveIT | https://www.biosolveit.de/flexx/index.html | |
| RosettaLigand [69] | Free/open source platform for academic license | https://www.rosettacommons.org/software | |
| CDOCKER [70] | Commercially available through BIOVIA | https://www.3dsbiovia.com/ | |
| SwissDock [71,72] | Free webserver | http://www.swissdock.ch/docking | |
| Pharmer [73] | Free/open source platform | http://smoothdock.ccbb.pitt.edu/pharmer/ | |
| CATALYST [74] | Commercially available through BIOVIA | https://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/pharmacophore-and-ligand-based-design.html | |
| PharmGist [75] | Free webserver | http://bioinfo3d.cs.tau.ac.il/pharma/php.php | |
| LigandScout [76] | Commercially available through Inte:Ligand | http://www.inteligand.com/ligandscout/ | |
| SwissSimilarity [77] | Free webserver | http://www.swisssimilarity.ch/ | |
| LEA3D [78] | Free webserver | https://chemoinfo.ipmc.cnrs.fr/LEA3D/index.html | |
| PyRx [79] | Free (no support) or commercially available | https://pyrx.sourceforge.io/ | |
| Phase [80] | Commercially available through Schrödinger | https://www.schrodinger.com/phase | |
| Molecular Dynamics | AMBER [81,82] | Commercially available | https://ambermd.org/ |
| CHARMM [83] | Free or commercially available through CHARMM or BIOVIA |
http://charmm.chemistry.harvard.edu/
https://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/simulations.html |
|
| CHARMMing [84] | Free webserver | https://www.charmming.org/charmming | |
| GROMACS [85,86] | Free/open source platform | http://www.gromacs.org/ | |
| NAMD [87] | Free/open source platform | https://www.ks.uiuc.edu/Research/namd/ | |
| Desmond [88] | Commercially available through Schrödinger | https://www.schrodinger.com/desmond | |
| SwissParam [89] | Free webserver | http://www.swissparam.ch/ | |
| CHARMM-GUI [90] | Free webserver | http://www.charmm-gui.org/ | |
| ParamChem CGenFF [91,92,93] | Free webserver | https://cgenff.umaryland.edu/ | |
| VMD [94] | Free/open source platform | https://www.ks.uiuc.edu/Research/vmd/ | |
| Molecular Descriptors, Fingerprints, and Quantitative Structure-Activity Relationship | Dragon [95] | Commercially available through Talete | http://www.talete.mi.it/products/dragon_description.htm |
| E-Dragon [96] | Free webserver | http://146.107.217.178/lab/edragon/start.html | |
| Canvas [97] | Commercially available through Schrödinger | https://www.schrodinger.com/canvas | |
| RDKit [98] | Free/open source platform | https://www.rdkit.org/docs/source/rdkit.ML.Descriptors.MoleculeDescriptors.html | |
| PyDescriptor [99] | Free/open source platform | https://ochem.eu/home/show.do | |
| Mordred [100] | Free/open source platform | https://github.com/mordred-descriptor/mordred | |
| Open3DQSAR [101] | Free/open source platform | http://open3dqsar.sourceforge.net/?Home | |
| ChemSAR [102] | Free webserver | http://chemsar.scbdd.com/ | |
| SeeSAR [103] | Commercially available through BioSolveIT | https://www.biosolveit.de/SeeSAR/ | |
| Pharmacokinetic properties | QikProp [104] | Commercially available through Schrödinger | https://www.schrodinger.com/qikprop |
| ADMET Predictor [105] | Commercially available through SimulationsPlus, Inc. | https://www.simulations-plus.com/software/overview/ | |
| ACD Percepta [106] | Commercially available through ACD/Labs | https://www.acdlabs.com/products/percepta/index.php | |
| FAF-Drugs4 [107] | Free webserver | http://fafdrugs4.mti.univ-paris-diderot.fr/ | |
| PatchSearch [108] | Free webserver | http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PatchSearch | |
| TOPKAT [109] and ADMET [110] | Commercially available through BIOVIA | https://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/qsar-admet-and-predictive-toxicology.html | |
| PASS Online [111] | Free webserver or commercially available standalone program | http://pharmaexpert.ru/Passonline/index.php | |
| SwissADME [112] | Free webserver | http://www.swissadme.ch/ | |
| MetaSite [113] | Commercially available through Molecular Discovery | https://www.moldiscovery.com/software/metasite/ | |
| ToxPredict [114] | Free webserver | https://apps.ideaconsult.net/ToxPredict# | |
| VirtualToxLab [115,116,117,118] | Free standalone software | http://www.biograf.ch/index.php?id=home | |
| admetSAR [119,120,121] | Free webserver | http://lmmd.ecust.edu.cn/admetsar1/home/ | |
| MetaTox [122,123] | Free webserver | http://way2drug.com/mg2/ |
More available tools and detailed descriptions for the programs and servers can be found at https://www.click2drug.org/.