Fragment-based docking: Development of the CHARMMing Web user interface as a platform for Computer-Aided Drug Design

Yuri Pevzner , Emilie Frugier , Vinushka Schalk , Amedeo Caflisch , and H. Lee Woodcock
J. Chem. Inf. Model., Just Accepted Manuscript

Abstract
Web-based front end interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), allows researcher to take advantage of the functionality of the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multi-scale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly on the CHARMMing Web server or on local HPC resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-docking's" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

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