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