Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 2, Issue 3, Pages 464-471Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct050307u
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Funding
- NIGMS NIH HHS [R01 GM067801-05, R01 GM067801, R01 GM067801-06A1] Funding Source: Medline
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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.
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