Identifying the Hierarchy of Dynamic Domains in Proteins Using the Data of Molecular Dynamics Simulations

Semen   O.   Yesylevskyy

doi:10.2174/092986610790963636

Abstract

The Hierarchical Domain-Wise Alignment (HDWA) technique of domain identification in proteins is presented. HDWA is designed to identify hierarchically organized dynamic domains in proteins using the MD trajectories by eliminating systematic motions from MD trajectories recursively in a model-free manner. The method is tested on the proteins from different structural classes.

Keywords: Domain identification, dynamic domains, hierarchy of domains, hierarchical domain-wise alignment, molecular dynamics, protein domains

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Protein & Peptide Letters

Title: Identifying the Hierarchy of Dynamic Domains in Proteins Using the Data of Molecular Dynamics Simulations

Volume: 17 Issue: 4

Author(s): Semen O. Yesylevskyy

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Keywords: Domain identification, dynamic domains, hierarchy of domains, hierarchical domain-wise alignment, molecular dynamics, protein domains

Abstract: The Hierarchical Domain-Wise Alignment (HDWA) technique of domain identification in proteins is presented. HDWA is designed to identify hierarchically organized dynamic domains in proteins using the MD trajectories by eliminating systematic motions from MD trajectories recursively in a model-free manner. The method is tested on the proteins from different structural classes.

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Yesylevskyy O. Semen, Identifying the Hierarchy of Dynamic Domains in Proteins Using the Data of Molecular Dynamics Simulations, Protein & Peptide Letters 2010; 17 (4) . https://dx.doi.org/10.2174/092986610790963636