Solving a Generalized Distance Geometry Problem for Protein Structure Determination |
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Authors: | Atilla Sit Zhijun Wu |
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Institution: | (1) Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020, USA;(2) Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA;(3) Department of Mathematics, Iowa State University, Ames, IA 50011, USA;(4) Department of Computer Science, Iowa State University, Ames, IA 50011, USA;(5) Laboratory of Theory of Biopolymers, Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland;(6) Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland |
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Abstract: | We propose a new approach to the problem of determining an ensemble of protein structures with a set of interatomic distance
bounds in NMR protein modeling. Similarly to X-ray crystallography, we assume that the protein has an equilibrium structure
and the atoms fluctuate around their equilibrium positions. Then, the problem can be formulated as a generalized distance
geometry problem, to find the equilibrium positions and maximal possible fluctuation radii for the atoms in the protein, subject
to the condition that the fluctuations should be within the given distance bounds. We describe the scientific background of
the work, the motivation of the new approach and the formulation of the problem. We develop a geometric buildup algorithm
for an approximate solution to the problem and present some preliminary test results as a first step concept proofing. We
also discuss related theoretical and computational issues and potential impacts of this work in NMR protein modeling. |
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