Dynamics based clustering of globin family members.

ABSTRACT: A methodology to cluster proteins based on their dynamics' similarity is presented. For each pair of proteins from a dataset, the structures are superimposed, and the Anisotropic Network Model modes of motions are calculated. The twelve slowest modes from each protein are matched using a local mode alignment algorithm based on the local sequence alignment algorithm of Smith-Waterman. The dynamical similarity distance matrix is calculated based on the top scoring matches of each pair and the proteins are clustered using a hierarchical clustering algorithm. The utility of this method is exemplified on a dataset of protein chains from the globin family and a dataset of tetrameric hemoglobins. The results demonstrate the effect of the quaternary structure of globin members on their intrinsic d

SUBMITTER: Tobi D 

PROVIDER: S-EPMC6279032 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature