Including ligand-induced protein flexibility into protein tunnel prediction
نویسندگان
چکیده
منابع مشابه
Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes
Computational prediction of ligand entry and egress paths in proteins has become an emerging topic in computational biology and has proven useful in fields such as protein engineering and drug design. Geometric tunnel prediction programs, such as Caver3.0 and MolAxis, are computationally efficient methods to identify potential ligand entry and egress routes in proteins. Although many geometric ...
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quency motions, the so called "essential" degrees of freedom [1, 2], which typically appear in timescales of nanoseconds to microseconds and play important roles in signalling, activation and enzyme function. Despite the rapid growth of computer power these timescales are not accessible with current molecular dynamic simulations systems. The CONCOORD system attempts to alleviate this sampling p...
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The “lock-and-key” model emphasizes the importance of shape complementarity between two rigid structures. It can not be used to explain the conformation changes before and after binding. The “induced fit” model considers the conformation change due to non-rigid protein interactions. A geometric fit is ensured only after the structure rearrangement of the base protein. In the preexisting equilib...
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The results of a thermodynamic calculation of the excess heat capacity that is based on experimental observations and that incorporates the effects of ligand binding on the two-state, thermal denaturation of a protein are presented. For a protein with a single-binding site on the native species and at subsaturating concentrations of ligand, bimodal or unimodal thermograms were computed merely b...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2014
ISSN: 0192-8651
DOI: 10.1002/jcc.23680