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An extended dead‐end elimination algorithm to determine gap‐free lists of low energy states
Author(s) -
Kloppmann Edda,
Ullmann G. Matthias,
Becker Torsten
Publication year - 2007
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20749
Subject(s) - bacteriorhodopsin , protonation , pairwise comparison , algorithm , state (computer science) , energy (signal processing) , chemistry , physics , proton , function (biology) , computational chemistry , computer science , quantum mechanics , ion , artificial intelligence , membrane , evolutionary biology , biology , biochemistry
Abstract Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified. We introduce an algorithm that allows the determination of a gap‐free list of the low energy states. This algorithm is based on the dead‐end elimination (DEE) theorem and is termed X‐DEE (extended DEE). X‐DEE is applicable to discrete systems whose state energy can be formulated as pairwise interaction between sites and their intrinsic energies. In this article, the computational performance of X‐DEE is analyzed and discussed. X‐DEE is implemented to determine the lowest energy protonation states of proteins, a problem to which DEE has not been applied so far. We use X‐DEE to calculate a list of low energy protonation states for two bacteriorhodopsin structures that represent the first proton transfer step of the bacteriorhodopsin photocycle. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007