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A New Method for Coarse-Grained Elastic Normal-Mode Analysis.

ABSTRACT: In this paper, we report a new method for coarse-grained elastic normal-mode analysis. The purpose is to overcome a long-standing problem in the conventional analysis called the tip effect that makes the motional patterns (eigenvectors) of some low-frequency modes irrational. The new method retains the merits of a conventional method such as not requiring lengthy initial energy minimization, which always distorts structures, and also delivers substantially more accurate low-frequency modes with no tip effect for proteins of any size. This improvement of modes is crucial for certain types of applications such as structural refinement or normal-mode-based sampling.

SUBMITTER: Lu M

PROVIDER: S-EPMC3133770 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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A New Method for Coarse-Grained Elastic Normal-Mode Analysis.

Lu Mingyang M Poon Billy B Ma Jianpeng J

Journal of chemical theory and computation 20060101 3

In this paper, we report a new method for coarse-grained elastic normal-mode analysis. The purpose is to overcome a long-standing problem in the conventional analysis called the tip effect that makes the motional patterns (eigenvectors) of some low-frequency modes irrational. The new method retains the merits of a conventional method such as not requiring lengthy initial energy minimization, which always distorts structures, and also delivers substantially more accurate low-frequency modes with ...[more]

PMID: 21760758

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