Loksha, Ilya V. and Maiolo, James R., III and Hong, Cheng W. and Ng, Albert and Snow, Christopher D. (2009) SHARPEN - Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network. Journal of Computational Chemistry, 30 (6). pp. 999-1005. ISSN 0192-8651 http://resolver.caltech.edu/CaltechAUTHORS:20090529-093039535
- Published Version
Restricted to Repository administrators only
See Usage Policy.
Use this Persistent URL to link to this item: http://resolver.caltech.edu/CaltechAUTHORS:20090529-093039535
Algorithms for discrete optimization of proteins play a central role in recent advances in protein structure prediction and design. We wish to improve the resources available for computational biologists to rapidly prototype such algorithms and to easily scale these algorithms to many processors. To that end, we describe the implementation and use of two new open source resources, citing potential benefits over existing software. We discuss CHOMP, a new object-oriented library for macromolecular optimization, and SHARPEN, a framework for scaling CHOMP scripts to many computers. These tools allow users to develop new algorithms for a variety of applications including protein repacking, protein-protein docking, loop rebuilding, or homology model remediation. Particular care was taken to allow modular energy function design; protein conformations may currently be scored using either the OPLSaa molecular mechanical energy function or an all-atom semiempirical energy function employed by Rosetta.
|Additional Information:||© 2009 Wiley Periodicals, Inc. Received 13 October 2008; Accepted 5 December 2008. Published online 23 January 2009. The authors thank Frances H. Arnold for supporting the project; the Jane Coffin Childs foundation and KAUST for postdoctoral support of C.D.S; Mani Chandy for teaching the Distributed Systems course; Jason Paryani for porting the CCD code; Ram Kandasamy for implementing amino acid variants; Phillip Romero and Ben Allen for helpful discussions; Vijay Pande for access to the Folding@Home code; and David Baker for access to the Rosetta code.|
|Subject Keywords:||protein-structure prediction; object-oriented programming; rotamer optimization; distributed computing; Folding@Home|
|Usage Policy:||No commercial reproduction, distribution, display or performance rights in this work are provided.|
|Deposited By:||Tony Diaz|
|Deposited On:||25 Aug 2009 23:17|
|Last Modified:||26 Dec 2012 11:02|
Repository Staff Only: item control page