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