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Nucleic Acids Research Advance Access published online on June 13, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn367
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

LocalMove: computing on-lattice fits for biopolymers

Y. Ponty, R. Istrate, E. Porcelli and P. Clote*

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA

*To whom correspondence should be addressed. Tel: +1 617 552 1332; Fax: +1 617 552 2011; Email: clote{at}bc.edu

Received . Revised May 21, 2008. Accepted May 22, 2008.

Given an input Protein Data Bank file (PDB) for a protein or RNA molecule, LocalMove is a web server that determines an on-lattice representation for the input biomolecule. The web server implements a Markov Chain Monte-Carlo algorithm with simulated annealing to compute an approximate fit for either the coarse-grain model or backbone model on either the cubic or face-centered cubic lattice. LocalMove returns a PDB file as output, as well as dynamic movie of 3D images of intermediate conformations during the computation. The LocalMove server is publicly available at http://bioinformatics.bc.edu/clotelab/localmove/.


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