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A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.

ABSTRACT: In this article, we report a method for coarse-grained normal mode analysis called the minimalist network model. The main features of the method are that it can deliver accurate low-frequency modes on structures without undergoing initial energy minimization and that it also retains the details of molecular interactions. The method does not require any additional adjustable parameters after coarse graining and is computationally very fast. Tests on modeling the experimentally measured anisotropic displacement parameters in biomolecular x-ray crystallography demonstrate that the method can consistently perform better than other commonly used methods including our own one. We expect this method to be effective for applications such as structural refinement and conformational sampling.

SUBMITTER: Lu M

PROVIDER: S-EPMC2563068 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature

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A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.

Lu Mingyang M Ma Jianpeng J

Proceedings of the National Academy of Sciences of the United States of America 20081001 40

In this article, we report a method for coarse-grained normal mode analysis called the minimalist network model. The main features of the method are that it can deliver accurate low-frequency modes on structures without undergoing initial energy minimization and that it also retains the details of molecular interactions. The method does not require any additional adjustable parameters after coarse graining and is computationally very fast. Tests on modeling the experimentally measured anisotropi ...[more]

PMID: 18832168

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