ProgramWebsiteReference
AMMOS2http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.phpLabbé C., Pencheva T., Jereva D., Desvillechabrol D., Becot J., Villoutreix B. O., Pajeva I., Miteva M. A., AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics. Nucleic Acids Research, 2017, 45, W350–W355.
AutoDock CrankPephttps://ccsb.scripps.edu/adcp/AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes. Bioinformatics, 2019, 35, 5121–5127.
AutoDock Vinahttps://github.com/ccsb-scripps/AutoDock-VinaEberhardt J., Santos-Martins D., Tillack A. F., Forli S., AutoDock Vina 1.2.0: New docking methods, expanded force field, and Python bindings. Journal of Chemical Information and Modeling, 2021, 61, 3891–3898.
B-AceP toolhttp://www4g.biotec.or.th/FeptideDB/ligand_docking.phpPanyayai T., Ngamphiw C., Tongsima S., Mhuantong W., Limsripraphan W., Choowongkomon K., Sawatdichaikul O., FeptideDB: A web application for new bioactive peptides from food protein. Heliyon, 2019, 5, e02076.
BINANAhttps://durrantlab.pitt.edu/binana/BINANA 2: Characterizing receptor/ligand interactions in Python and JavaScript. Journal of Chemical Information and Modeling, 2022, 62, 753–760.
CABS-dockhttp://biocomp.chem.uw.edu.pl/CABSdockFlexible docking of peptides to proteins using CABS-dock. Protein Science, 2020, 29, 211–222.
CB-Dockhttp://clab.labshare.cn/cb-dock/php/Liu Y., Grimm M., Dai W., Hou M., Xiao Z.-X., Cao Y., CB-Dock: a web server for cavity detection-guided protein–ligand blind docking. Acta Pharmacologica Sinica, 2020, 41, 138–144.
CB-Dock2https://cadd.labshare.cn/cb-dock2/php/index.phpCB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Research, 2022, 50, W159–W164.
CB-DOCK3https://cadd.labshare.cn/cb-dock3/php/index_v3.phpCB-Dock3: an enhanced web server for protein–ligand blind docking. Nucleic Acids Research, 2026, 54, W238–W245.
ClusProhttps://cluspro.org/login.php?redir=/home.phpAlekseenko A., Kotelnikov S., Ignatov M., Egbert M., Kholodov Y., Vajda S., Kozakov D., ClusPro LigTBM: automated template-based small molecule docking. Journal of Molecular Biology, 2020, 432, 3404-3410.
Coachhttps://zhanggroup.org/COACH/Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 2013, 29, 2588-2595.
Coach-Dhttps://yanglab.qd.sdu.edu.cn/COACH-D/Wu Q., Peng Z., Zhang Y., Yang J., COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking. Nucleic Acids Research, 2018, 46, W438–W442.
CovalentDock Cloudhttp://docking.sce.ntu.edu.sg/Ouyang X. Zhou S., Ge Z., Li R., Kwoh C. K., CovalentDock Cloud: a web server for automated covalent docking. Nucleic Acids Research, 2013, 41, W329-W332.
COVID-19 Docking Serverhttps://ncov.schanglab.org.cn/index.phpKong R., Yang G. B., Xue R., Liu M., Wang F., Hu J. P., Guo X. Q., Chang S., COVID-19 Docking Server: An interactive server for docking small molecules, peptides and antibodies against potential targets of COVID-19. Bioinformatics, 2020, 36, 5109–5111.
DockThorhttps://www.dockthor.lncc.br/v2/Santos K. B., Guedes I. A., Karl A. L. M., Dardenne L. E., Highly flexible ligand docking: benchmarking of the DockThor program on the LEADS-PEP protein–peptide data set. Journal of Chemical Information and Modeling, 2020, 60, 667-683.
EDockhttps://zhanggroup.org//EDock/Zhang W., E. W., Yin M., Zhang Y., EDock: blind protein–ligand docking by replica‑exchange Monte Carlo simulation. Journal of Cheminformatics, 2020, 12, 37.
FitDockhttp://cao.labshare.cn/fitdock/php/index.phpYang X., Liu Y., Gan J., Xiao Z.-X., Cao Y., FitDock: protein–ligand docking by template fitting. Briefings in Bioinformatics, 2022, 23, bbac087.
GalaxyPEPDOCKhttp://galaxy.seoklab.org/cgi-bin/submit.cgi?type=PEPDOCKLee H., Heo L., Lee M. S., Seok C., GalaxyPepDock: A protein-peptide docking tool based on interaction similarity and energy optimization. Nucleic Acids Research, 2015, 43, W431-W435.
HawkDockhttp://cadd.zju.edu.cn/hawkdock/Zhang X., Jiang L., Weng G., Shen C., Zhang O., Liu M., Zhang C., Gu S., Wang J., Wang X., Du H., Zhang H., Zhang K., Wang E., Hou T., HawkDock version 2: an updated web server to predict and analyze the structures of protein–protein complexes. Nucleic Acids Research, 2025, 53, W306–W315.
HCovDockhttp://huanglab.phys.hust.edu.cn/hcovdock/Wu Q., Huang S. Y., HCovDock: an efficient docking method for modeling covalent protein–ligand interactions. Briefings in Bioinformatics, 2023, 24, bbac559.
Hexhttp://hex.loria.fr/
http://hexserver.loria.fr/		Macindoe G., Mavridis L., Venkatraman V., Devignes M.-D., Ritchie D. W., HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Research, 2010, 38, W445-W449.
HPEPDOCKhttp://huanglab.phys.hust.edu.cn/hpepdock/Zhou P., Jin B., Li H., Huang S-Y., HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Research, 2018, 46, W443-W450.
InstaDockhttps://hassanlab.org/instadock/Mohammad T., Mathur Y., Hassan M. I., InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening. Briefings in Bioinformatics, 2021, 22, Article No bbaa279.
MDockPep2https://zougrouptoolkit.missouri.edu/mdockpep2/index.htmlPredicting protein–peptide complex structures by accounting for peptide flexibility and the physicochemical environment. Journal of Chemical Information and Modeling, 2022, 62, 27-39.
MetaDockhttp://www.hpppi.iicb.res.in/metadock/index.htmlKamal I. M., Chakrabarti S., MetaDOCK: A combinatorial molecular docking approach. ACS Omega, 2023, 8, 5850−5860.
ML-PLIChttp://cadd.zju.edu.cn/plic/Zhang X., Shen C., Wang T., Deng Y., Kang Y., Li D., Hou T., Pan P., ML-PLIC: a web platform for characterizing protein–ligand interactions and developing machine learning-based scoring functions. Briefings in Bioinformatics, 2023, 24, bbad295.
MolModahttps://durrantlab.pitt.edu/molmoda/#Kochnev Y., Ahmed M., Maldonado A. M., Durrant J. D., MolModa: accessible and secure molecular docking in a web browser. Nucleic Acids Research, 2024, 52, W498–W506.
nCoVDock2https://ncovdock2.schanglab.org.cn/Liu K., Lu X., Shi H., Xu X., Kong R., Chang S., nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands. Nucleic Acids Research, 51, 2023, 51, W365–W371.
ParDOCK+http://www.scfbio-iitd.res.in/pardock+/Jayaram B., Singh T., Mukherjee G., Mathur A., Shekhar S., Shekhar V., Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics, 2012, 13 (Suppl 17), S7.
PepATTRACThttps://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT/#overviewde Vries S. J., JRey J., Schindler C. E. M., Zacharias M., Tuffery P., The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Research, 2017, 45, W361-W364.
PIPER-FlexPepDockhttp://piperfpd.furmanlab.cs.huji.ac.il/Alam N., Goldstein O., Xia B., Porter K., Kozakov D., Schueler-Furman O., High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PLoS Computational Biology, 2017, 13, e1005905.
PPDbenchhttps://webs.iiitd.edu.in/raghava/ppdbench/Agrawal P., Singh H., Srivastava H. K., Singh S., Kishore G., Raghava G. P. S., Benchmarking of different molecular docking methods for protein-peptide docking. BMC Bioinformatics, 2019, 19, 426.
ProBis-Dockhttp://insilab.org/probisdock/Konc J., Lešnik S., Škrlj B., Sova M., Proj M., Knez D., Gobec S., Janežič D., ProBiS-Dock: a hybrid multitemplate homology flexible docking algorithm enabled by protein binding site comparison. Journal of Chemical Information and Modeling, 2022, 62, 1573–1584.
ProteinsPlushttps://proteins.plus/Ehrt C., Schulze T., Graef J., Diedrich K., Pletzer-Zelgert J., Rarey M., Proteins Plus: a publicly available resource for protein structure mining. Nucleic Acids Research, 2025, 53, W478–W484.
SwissDockhttp://www.swissdock.ch/Bugnon M., Röhrig U. F., Goullieux M., Perez M. A. S., Daina A., Michielin O., Zoete V., SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Research, 2024, 52, W324–W332.
systemsDockhttp://systemsdock.unit.oist.jp/iddp/home/indexHsin K.-Y., Matsuoka Y., Asai Y., Kamiyoshi K., Watanabe T., Kawaoka Y., Kitano H., systemsDock: a web server for network pharmacology-based prediction and analysis. Nucleic Acids Research, 2016, 44, W507–W513.
UNRES serverhttp://unres-server.chem.ug.edu.pl/login/?next=/Krupa P., Karczyńska A. S., Mozolewska M. A., Liwo A., Czaplewski C., UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations. Bioinformatics, 2021, 37, 1613–1615.
Webinahttps://durrantlab.pitt.edu/webina/Kochnev Y., Hellemann E., Cassidy K. C., Durrant J. D., Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. Bioinformatics, 2020, 36, 4513–4515.
ZDOCKhttps://zdock.umassmed.edu/Pierce B. G., Wiehe K., Hwang H., Kim B. H., Vreven T., Weng Z., ZDOCK Server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics, 2014, 30, 1771-1773.