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. 2011 Jul;39(Web Server issue):W270-7.
doi: 10.1093/nar/gkr366. Epub 2011 May 29.

SwissDock, a Protein-Small Molecule Docking Web Service Based on EADock DSS

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Free PMC article

SwissDock, a Protein-Small Molecule Docking Web Service Based on EADock DSS

Aurélien Grosdidier et al. Nucleic Acids Res. .
Free PMC article

Abstract

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.

Figures

Figure 1.
Figure 1.
(A) Screenshot of the job submission form. It is dynamically modified so that the user can replace the default target selection from PDB codes by a target upload form (B). Similarly, the default ligand selection from ZINC codes can be replaced either by a ligand upload form (C) or by a fragment selection form (D) if a screening assay is to be performed. In such a case, the fragments to dock can be manually selected (E). The contextual help is automatically adapted to submission form content.
Figure 2.
Figure 2.
This figure shows a typical output of SwissDock for the docking of the Guanine nucleotide-binding protein G(q) subunit alpha, a target involved in uveal melanoma (35). (A) Screenshot of the Jmol applet which renders predicted BMs within the web browser. (B) Visual investigation using the ViewDock plugin of UCSF Chimera. The predicted BM of the guanosine diphosphate (magenta sticks) is superimposed to the X-ray BM (ball and sticks). As it can be seen in the lower part of the figure, this particular predicted BM has the most favorable energy.
Figure 3.
Figure 3.
Sequence diagram of a typical interaction between a SwissDock SOAP client and the SwissDock SOAP server. The target preparation, ligand preparation and docking submission tasks can be performed in a row or independently. Each task is divided into three steps. First, the client submits the task. Second, it polls the server at regular intervals in order to know if the task has been processed. If so, the outcome of the task is retrieved from the server.

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