SwissDock, a protein-small molecule docking web service based on EADock DSS
Open accessAbstract
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.
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A computational model based on the quantitative structure-activity relationship (QSAR) can swiftly predict vast numbers of compounds or superficial physicochemical characteristics like log P or log D.
“A computational model based on the quantitative structure-activity relationship (QSAR) can swiftly predict vast numbers of compounds or superficial physicochemical characteristics like log P or log D”
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- Authors
- Grosdidier, A., Zoete, V., & Michielin, O.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- Corresponding author
- Zoete, V.
- Michielin, O.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-05-29
- Volume
- 39
- Issue
- suppl
- Pages
- W270-W277
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3125772
- OpenAlex
- W2101078720
- Cited by
- 1,950
- References
- 31
- Citations by year
- 2026: 137 · 2025: 190 · 2024: 190 · 2023: 214 · 2022: 186 · 2021: 225 · 2020: 195 · 2019: 150 · 2018: 106 · 2017: 110 · 2016: 80 · 2015: 67 · 2014: 45 · 2013: 35 · 2012: 16
- FWCI
- 30.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- reroDoc Digital Library (submittedVersion)
- IRIS (submittedVersion, other-oa)
- SERVAL (Université de Lausanne) (submittedVersion, other-oa)
- Funders
- National Science Foundation (RR001081, 310030)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (103173, 130857, 103172, 3200B0, 310030)
- Oncosuisse
- National Institutes of Health (RR001081)
- University of California, San Francisco
- National Center for Research Resources (P41RR001081)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- web server, molecular docking, drug design, ligand preparation, protein-ligand complex prediction
- MeSH terms
- Ligands, Models, Molecular, Protein Conformation, Software, Drug Design, Protein Engineering, Internet
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