Reliable protein structure refinement using a physical energy function
نویسندگان
چکیده
منابع مشابه
Protein folding using fragment assembly and physical energy function.
We perform a systematic study of the effects of sequence-independent backbone interactions and sequence-dependent side-chain interactions on protein folding using fragment assembly and physical energy function. Structures for ten proteins belonging to various structural classes are predicted only with Lennard-Jones interaction between backbone atoms. We find nativelike structures for beta prote...
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We have recently described a new conformational search strategy for protein folding algorithms called the CGU (convex global underestimator) method. Here we use a simplified protein chain representation and a differentiable form of the Sun/Thomas/Dill energy function to test the CGU method. Standard search methods, such as Monte Carlo and molecular dynamics are slowed by kinetic traps. That is,...
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One of the greatest shortcomings of macromolecular energy minimization and molecular dynamics techniques is that they generally do not preserve the native structure of proteins as observed by x-ray crystallography. This deformation of the native structure means that these methods are not generally used to refine structures produced by homology-modeling techniques. Here, we use a database of 75 ...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2010
ISSN: 0192-8651
DOI: 10.1002/jcc.21664