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

LocalMove: computing on-lattice fits for biopolymers

Y Ponty  1 , R Istrate, E Porcelli, P Clote
Affiliations

LocalMove: computing on-lattice fits for biopolymers

Y Ponty et al. Nucleic Acids Res. .

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/.

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Figures

Figure 1.
Figure 1.
Backbones of protein (left) and RNA (right). Note that residue resp. nucleotide positions increase from the bottom of the figure towards the top.
Figure 2.
Figure 2.
Neighbors of a point under various lattice models: (left) 3D cubic lattice, (middle) 3D FCC, (right) numbers of self-avoiding walks of various sizes on FCC. The FCC lattice can be represented as the set of all integral coordinates (x,y,z), such that formula image. If p = (x,y,z) and q = (a,b,c), then p,q are immediate neighbors if formula image, and |x − a|,|y − b|,|z − c| ≤ 1. Note that immediate neighbors on the FCC lattice are at Euclidean distance formula image from each other, hence comparisons with PDB data are made after normalization that ensures unit distance between successive monomers.
Figure 3.
Figure 3.
(Left) Distribution of cRMS for LocalMove best on-lattice fits for the backbones (O5′,P,O3′,C5′,C4′,C3′) of 1735 RNA models/chains from the NDB, superimposed with the (normalized) NDB files. Statistics for cRMS: mean is 0.554169, SD is 0.145392, both measured in lattice units. (Right) Distribution of cRMS for LocalMove best on-lattice fits for the backbone (N,Cα,C) of 1733 (monochain) proteins from PDBselect25 (20), a nonredundant protein database (pairwise, proteins have at most 25% sequence identity), superimposed with the (normalized) original PDB files. Statistics for cRMS: mean is 0.612181, SD is 0.161009.
Figure 4.
Figure 4.
FCC lattice fits for the full backbone of two ribozymes models [PDB IDs 1SJ3:R (left panel) and 1GID:A (right panel)] superimposed with their original models.
Figure 5.
Figure 5.
Screen shot of LocalMove web server.
See this image and copyright information in PMC

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