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LocalMove: computing on-lattice fits for biopolymers.

ABSTRACT: 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/.

SUBMITTER: Ponty Y

PROVIDER: S-EPMC2447748 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature

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LocalMove: computing on-lattice fits for biopolymers.

Ponty Y Y Istrate R R Porcelli E E Clote P P

Nucleic acids research 20080613 Web Server issue

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 conformatio ...[more]

PMID: 18556754

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