Biopolym. Cell. 2010; 26(2):146-152.
New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations
1Yesylevskyy S. O.
  1. Institute of Physics, NAS of Ukraine
    46, Prospect Nauki, Kyiv, Ukraine, 03028


Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD) simulations. The aim of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA) to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed.
Keywords: dynamic domains, domain identification, Hierarchical Domain-Wise Alignment, molecular dynamics


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