%0 Journal Article
%T Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains
%A Martin Mann
%A Rhodri Saunders
%A Cameron Smith
%A Rolf Backofen
%A Charlotte M. Deane
%J Advances in Bioinformatics
%D 2012
%I Hindawi Publishing Corporation
%R 10.1155/2012/148045
%X 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£¿£¿ 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. 1. Introduction It is not always computationally feasible to undertake protein structure studies using full atom representations. The challenge is to reduce complexity while maintaining detail [1¨C3]. Lattice protein models are often used to achieve this but in general only the protein backbone or the amino acid centre of mass is represented [4¨C12]. A huge variety of lattices and energy functions have previously been developed and applied [4, 13, 14]. In order to evaluate the applicability of different lattices and to enable the transformation of real protein structures into lattice models, a representative lattice protein structure has to be calculated. Ma uch and Gaur have shown the NP completeness of this problem for backbone-only models in the 3D-cubic lattice and named it the protein chain lattice fitting (PCLF) problem [15]. The PCLF problem has been widely studied for backbone-only models [13, 16¨C24]. The most important aspects in producing lattice protein models with a low root mean squared deviation (RMSD) are the lattice coordination number and the neighbourhood vector angles [18, 23]. Lattices with intermediate coordination numbers, such as the face-centred cubic (FCC) lattice, can produce high resolution backbone models [18] and have been used in many protein structure studies (e.g., [3, 25, 26]). However, the use of backbone models is
%U http://www.hindawi.com/journals/abi/2012/148045/