ProgramWebsiteReference
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.
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 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.
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.
BINANAhttps://durrantlab.pitt.edu/binana/Young J., Garikipati N., Durrant J. D., BINANA 2: Characterizing receptor/ligand interactions in Python and JavaScript. Journal of Chemical Information and Modeling, 2022, 62, 753–760.
ClusProhttps://cluspro.org/login.php?redir=/home.phpKozakov D., Hall D. R., Xia B., Porter K. A., Padhorny D., Yueh C., Beglov D., Vajda S., The ClusPro web server for protein-protein docking. Nature Protocols, 2017, 12, 255-278.
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, Article No 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, Article No 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/Weng G. Q., Wang E. C., Wang Z., Liu H., Li D., Zhu F., Hou T. J., HawkDock: a web server to predict and analyze the structures of protein-protein complexes based on computational docking and MM/GBSA. Nucleic Acids Research, 2019, 47, W322-W330.
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.
Hexhttp://hex.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.
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.
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, Article No e1005905.
ProteinsPlushttps://proteins.plus/Schöning-Stierand K., Diedrich K., Fährrolfes R., Flachsenberg F., Meyder A., Nittinger E., Steinegger R., Rarey M., ProteinsPlus: interactive analysis of protein–ligand binding interfaces. Nucleic Acids Research, 2020, 48, W48–W53.
SwissDockhttp://www.swissdock.ch/Grosdidier A., Zoete V., Michielin O., SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Research, 2011, 39, W270-W277.
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.