Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method.

ABSTRACT:

Background

Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new method that has the ability to detect transitions in dynamics based on the recurrences in the dynamical system. It combines bootstrapping and recurrence quantification analysis. We start from the assumption that a protein has a "baseline" recurrence structure over a given period of time. Any statistically significant deviation from this recurrence structure, as inferred from complexity measures provided by recurrence quantification analysis, is considered a transition

SUBMITTER: Karain WI 

PROVIDER: S-EPMC5704401 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature