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.
Bibliographical noteFunding Information:
We thank our Structural Bioinformatics Group and the system team of the Tel Aviv University Computer Science School. This research has been supported in part by the Center of Excellence in Geometric Computing and its Applications funded by the Israel Science Foundation (administered by the Israel Academy of Sciences). The research of H.J.W. is partially supported by the Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University. The research of Y.I. has been supported by the Eshkol Fellowship funded by the Israeli Ministry of Science. The research of R.N. has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-12400. The content of this publication does not necessarily reflect the view or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. Funding to pay the Open Access publication charges for this article was provided by SAIC-Frederick, Inc.