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Advances in Bioinformatics
Volume 2012 (2012), Article ID 148045, 6 pages
http://dx.doi.org/10.1155/2012/148045
Research Article

Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains

1Bioinformatics, University of Freiburg, Georges-Köhler Allee 106, 79110 Freiburg im Breisgau, Germany
2Theoretical Biochemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria
3Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK

Received 4 April 2012; Accepted 18 June 2012

Academic Editor: Shandar Ahmad

Copyright © 2012 Martin Mann et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models.