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Nucleic Acids Research 2006 34(Web Server issue):W57-W62; doi:10.1093/nar/gkl039
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models

Yunho Jang, Jay I. Jeong1 and Moon K. Kim*

Department of Mechanical and Industrial Engineering, University of Massachusetts Amherst, MA 01003, USA 1 School of Mechanical and Automotive Engineering, Kookmin University Seoul, South Korea

*To whom correspondence should be addressed. Tel: +1 413 545 2357; Fax: +1 413 545 1027; Email: mkkim{at}ecs.umass.edu

Received October 28, 2005. Revised December 22, 2005. Accepted January 13, 2006.

UMass Morph Server (UMMS) has been developed for the broad impact on the study of molecular dynamics (MD). The elastic network model (ENM) of a given macromolecule has been proven as a useful tool for analyzing thermal behaviors locally and predicting folding pathways globally. UMMS utilizes coarse-grained ENMs at various levels. These simplifications remarkably save computation time compared with all-atom MD simulations so that one can bring down massive computational problems from a supercomputer to a PC. To improve computational efficiency and physical reality of ENMs, the symmetry-constrained, rigid-cluster, hybrid and chemical-bond ENMs have been developed and implemented at UMMS. One can request both harmonic normal mode analysis of a single macromolecule and anharmonic pathway generation between two conformations of a same molecule using elastic network interpolation at http://biomechanics.ecs.umass.edu/umms.html.


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