PatchDock and SymmDock: servers for rigid and symmetric docking
TLDR
Two freely available web servers for molecular docking that perform structure prediction of protein–protein and protein–small molecule complexes and the SymmDock method predicts the structure of a homomultimer with cyclic symmetry given theructure of the monomeric unit are described.Abstract:
Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at http://bioinfo3d.cs.tau.ac.il. The methods behind the servers are very efficient, allowing large-scale docking experiments.read more
Citations
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The ClusPro web server for protein-protein docking.
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GRAMM-X public web server for protein-protein docking
TL;DR: GRAMM-X and its web interface extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring and frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations.
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