SwissDock, a protein-small molecule docking web service based on EADock DSS

By Aurélien Grosdidier, Vincent Zoete, Olivier Michielin. 2011

1,756 citations recorded by the source corpus.

Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

SWISS-MODEL: homology modelling of protein structures and complexes (2018, neutral): “We include links to the RCSB (33), PDBsum (40), PDBe (41), CATH (42) and SwissDock (43).”
Structure-Based Virtual Screening: From Classical to Artificial Intelligence (2020, background): “…optimization (Gowthaman et al., 2015) and PSOVina (Ng et al., 2015); • Local search such as Autodock Vina (Trott and Olson, 2009), SwissDock/EADock (Grosdidier et al., 2011) and GlamDock (Tietze and Apostolakis, 2007); • Exhaustive search such as eHiTS ( Zsoldos et al., 2007); • Linear programming…”
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting (2022, methodology): “The state-of-the-art blind docking methods such as SwissDock (9), COACH-D (10), EDock (11), MTi-AutoDock (12) etc. have been extensively used in exploring potential binding sites or ligand-binding poses.”
Microbial Decolorization of an Azo Dye Reactive Black 5 Using White-Rot Fungus Pleurotus eryngii F032 (2013, methodology): “3.7 Docking of Reactive Black 5 and Tween 80 The SwissDock predicted 31 potential binding sites of RB5 and also generated about eight conformations for each of the binding site.”
SwissTargetPrediction: a web server for target prediction of bioactive small molecules (2014, methodology): “In future developments, SwissTargetPrediction will be further integrated with these tools, for instance by predicting potential binding modes with SwissDock (44).”
PLIP: fully automated protein–ligand interaction profiler (2015, background): “Cathepsin K in complex with a small molecule inhibitor (PDB ID 1VSN) was used for a redocking experiment using the SwissDock server at swissdock.ch .”
GOMoDo: A GPCRs Online Modeling and Docking Webserver (2013, background): “Both GPCR modeling servers/databases (GPCR-SSFE [12], GPCR-ITASSER [13], and GPCR-ModSim [14]) and small ligand docking servers exist (MEDock [15], PatchDock [16], and SwissDock [17]).”
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules (2019, methodology): “This set relies on the bioactivity data of ChEMBL version 23 (14,15) and thus describes more molecules and more targets than the old version (based on ChEMBL version 16).”