LocalMove: computing on-lattice fits for biopolymers

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W216-22. doi: 10.1093/nar/gkn367. Epub 2008 Jun 13.

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/.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Internet
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Protein Conformation*
  • RNA / chemistry*
  • Software*

Substances

  • RNA