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Surflex:  Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine

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UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California, San Francisco, California 94143-0128
Cite this: J. Med. Chem. 2003, 46, 4, 499–511
Publication Date (Web):January 21, 2003
https://doi.org/10.1021/jm020406h
Copyright © 2003 American Chemical Society
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    Abstract

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    Surflex is a fully automatic flexible molecular docking algorithm that combines the scoring function from the Hammerhead docking system with a search engine that relies on a surface-based molecular similarity method as a means to rapidly generate suitable putative poses for molecular fragments. Results are presented evaluating reliability and accuracy of dockings compared with crystallographic experimental results on 81 protein/ligand pairs of substantial structural diversity. In over 80% of the complexes, Surflex's highest scoring docked pose was within 2.5 Å root-mean-square deviation (rmsd), with over 90% of the complexes having one of the top ranked poses within 2.5 Å rmsd. Results are also presented assessing Surflex's utility as a screening tool on two protein targets (thymidine kinase and estrogen receptor) using data sets on which competing methods were run. Performance of Surflex was significantly better, with true positive rates of greater than 80% at false positive rates of less than 1%. Docking time was roughly linear in number of rotatable bonds, beginning with a few seconds for rigid molecules and adding approximately 10 s per rotatable bond.

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     Phone:  (415) 502−7242. Fax:  (415) 502-3179. E-mail:  [email protected]. Address for regular postal service:  UCSF Cancer Center, Box 0128, San Francisco, CA 94143-0128. Address for express mail:  UCSF Cancer Center, 2340 Sutter Street, #S336, San Francisco, CA 94115.

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