TBI-p-2012-4
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Titel:
Producing high-accuracy lattice models from protein atomic co-ordinates including side chains
Author(s):
Martin Mann and Rhodri Saunders and Cameron Smith and Rolf Backofen and Charlotte M. Deane
submitted to:
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. The program is freely
available for academic download and as a web-server:
http://cpsp.informatik.uni-freiburg.de/LatFit/
We tested LatFit's accuracy and speed using a large non-redundant 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 about 1.5A 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
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Last modified: 2008-10-22 12:23:11 fall