The Dead-End Elimination Method, Tryptophan Rotamers, and Fluorescence Lifetimes
نویسندگان
چکیده
منابع مشابه
Tryptophan fluorescence lifetimes in lysozyme.
Tryptophan fluorescence lifetimes at pH 2 and pH 8 have been obtained for lysozyme and for lysozyme derivatives in which tryptophan-62 or tryptophan-108 or both are nonfluorescent. The lifetimes range from about 0.5 ns to 2.8 ns for the various emitting tryptophans. The tryptophan lifetimes appear to increase with exposure of tryptophan to solvent, but intramolecular contacts, probably with cys...
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Soft neighborhood substitutability (SNS) is a powerful technique to automatically detect and prune dominated solutions in combinatorial optimization. Recently, it has been shown in [26] that enforcing partial SNS (PSNS) during search can be worthwhile in the context of Weighted Constraint Satisfaction Problems (WCSP). However, for some problems, especially with large domains, PSNS is still too ...
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MOTIVATION Dead-End Elimination (DEE) is a powerful algorithm capable of reducing the search space for structure-based protein design by a combinatorial factor. By using a fixed backbone template, a rotamer library, and a potential energy function, DEE identifies and prunes rotamer choices that are provably not part of the Global Minimum Energy Conformation (GMEC), effectively eliminating the m...
متن کاملTheoretical and algorithmical optimization of the dead-end elimination theorem.
The dead-end elimination theorem has proved to be a powerful method to reduce the theoretically accessible conformational space when modeling protein side chains by using a rotameric representation of possible conformations. In this work, theoretical details about variants to the original criterion are discussed. We also provide information on how the equations can be algorithmically implemente...
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Dead-end elimination (DEE) is a powerful theorem for selecting optimal protein side-chain orientations from a large set of discrete conformations. The present work describes a new approach to dead-end elimination that effectively splits conformational space into partitions to more efficiently eliminate dead-ending rotamers. Split DEE makes it possible to complete protein design calculations tha...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2003
ISSN: 0006-3495
DOI: 10.1016/s0006-3495(03)74617-7