Bioinformatics · 2013 · 291 citations · 7 references
Life SciencesBiochemistryBioinformaticsComputational BiologyProtein-protein InteractionsStructural BiologyMolecular DockingProtein DockingProtein StructureProtein-ligand DockingProtein-protein DockingProtein-protein Interaction ModelingComputational Protein-protein DockingDocking BenchmarkingFlexible DockingFlexible Protein-protein DockingGlobal DockingLow-energy ConformersProtein-protein Docking Benchmark DatasetsWeb Server Architecture
Abstract Summary: 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. Availability: The server is freely available and can be accessed at: http://bmm.cancerresearchuk.org/%7ESwarmDock/. Contact: Paul.Bates@cancer.org.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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Protein–protein docking benchmark version 4.0
Howook Hwang, Thom Vreven, Joël Janin et al. · Proteins Structure Function and Bioinformatics · 2010 · 486 citations · Full text