Biopolym. Cell. 2010; 26(4):311-316.
http://dx.doi.org/10.7124/bc.000165
Bioinformatics
Identification of hierarchy of dynamic domains in proteins: comparison of HDWA and HCCP techniques
1Yesylevskyy S. O.
  1. Institute of Physics, NAS of Ukraine
    46, Prospect Nauki, Kyiv, Ukraine, 03028

Abstract

Aim. There are several techniques for the identification of hierarchy of dynamic domains in proteins. The goal of this work is to compare systematically two recently developed techniques, HCCP and HDWA,on a set of proteins from diverse structural classes. Methods. HDWA and HCCP techniques are used. The HDWA technique is designed to identify hierarchically organized dynamic domains in proteins using the Molecular Dynamics (MD) trajectories, while HCCP utilizes the normal modes of simplified elastic network models. Results. It is shown that the dynamic domains found by HDWA are consistent with the domains identified by HCCP and other techniques. At the same time HDWA identifies flexible mobile loops of proteins correctly, which is hard to achieve with other model-based domain identification techniques. Conclusion. HDWA is shown to be a powerful method of analysis of MD trajectories, which can be used in various areas of protein science.
Keywords: Dynamic domains, domain identification, Hierarchical Domain-Wise Alignment, molecular dynamics
Full text: (PDF, in English)

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