Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data.
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ABSTRACT:
SUBMITTER: Kondrashov DA
PROVIDER: S-EPMC1578481 | biostudies-literature | 2006 Oct
REPOSITORIES: biostudies-literature
Publications
Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data.
Kondrashov Dmitry A DA Cui Qiang Q Phillips George N GN
Biophysical journal 20060804 8
Simple coarse-grained models, such as the Gaussian network model, have been shown to capture some of the features of equilibrium protein dynamics. We extend this model by using atomic contacts to define residue interactions and introducing more than one interaction parameter between residues. We use B-factors from 98 ultra-high resolution (<or=1.0 A) x-ray crystal structures to optimize the interaction parameters. The average correlation between Gaussian network-model fluctuation predictions and ...[more]
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