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Exact analytical loop closure in proteins using polynomial equations

delete1999-06-01
delete104
PRE
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W
William J. Wedemeyer
H
Harold A. Scheraga *
DOI:10.1002/(SICI)1096-987X(199906)20:8<819::AID-JCC8>3.0.CO;2-Ydelete
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摘要

摘要

En 中文
Loop closure in proteins has been studied actively for over 25 years. Using spherical geometry and polynomial equations, several loop-closure problems in proteins are solved exactly by reducing them to the determination of the real roots of a polynomial. Loops of seven, flight, and nine atoms are treated explicitly, including the tripeptide and disulfide-bonded loop-closure problems. The number of valid loop closures can be evaluated by the method of Sturm chains, which counts the number of real roots of a polynomial. Longer loops can be treated by three methods: by sampling enough dihedral angles to reduce the problem to a soluble loop-closure problem; by applying the loop-closure algorithm hierarchically; or by decimating the chain into independently moving rigid elements that can be reconnected using loop-closure algorithms. Applications of the methods to docking, homology modeling and NMR problems are discussed. (C) 1999 John Wiley & Sons, Inc.
Keyword:
loop closure
ring closure
rigid geometry
spherical geometry
resultants
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期刊

Journal of Computational Chemistry 封面图
Journal of Computational Chemistry
IF:
4.8
论文数:
7.1K
被引数:
6.1W

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