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][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][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][51][52]
|
Free/open source platform
|
https://github.com/Discngine/fpocket
|
CASTp [53,54,55][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][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][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][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][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,[116,115117,118]][116][117][118]
|
Free standalone software
|
http://www.biograf.ch/index.php?id=home
|
admetSAR [119,120,121][119][120][121]
|
Free webserver
|
http://lmmd.ecust.edu.cn/admetsar1/home/
|
MetaTox [122,123][122][123]
|
Free webserver
|
http://way2drug.com/mg2/
|