SwarmDock: a server for flexible protein–protein docking | Zendy

Mieczyslaw Torchala | Zendy; Iain H. Moal | Zendy; Raphaël A. G. Chaleil | Zendy; Juan FernándezRecio | Zendy; Paul A. Bates | Zendy

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SwarmDock: a server for flexible protein–protein docking

Author(s) -

Mieczyslaw Torchala,

Iain H. Moal,

Raphaël A. G. Chaleil,

Juan FernándezRecio,

Paul A. Bates

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt038

Subject(s) - docking (animal) , upload , computer science , web server , macromolecular docking , protein data bank (rcsb pdb) , computational biology , the internet , operating system , biology , biochemistry , medicine , nursing

Protein-protein interactions are central to almost all biological functions, and the atomic details of such interactions can yield insights into the mechanisms that underlie these functions. We present a web server that wraps and extends the SwarmDock flexible protein-protein docking algorithm. After uploading PDB files of the binding partners, the server generates low energy conformations and returns a ranked list of clustered docking poses and their corresponding structures. The user can perform full global docking, or focus on particular residues that are implicated in binding. The server is validated in the CAPRI blind docking experiment, against the most current docking benchmark, and against the ClusPro docking server, the highest performing server currently available.

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