JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories.

ABSTRACT:

Background

Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to determine PCA modes (eigenvectors) and their eigenvalues. Protein dynamics can be characterized in terms of Cartesian coordinates or internal distance pairs. In understanding protein dynamics, a comparison of trajectories taken from a set of proteins for similarity assessment provides insight into conserved mechanisms. Comprehensive software is needed to facilitate comparative-analysis with user-friendly features that are rooted in best practices from multivariate statistics.

Results

We developed a Java based Essential Dynamics toolkit c

SUBMITTER: David CC 

PROVIDER: S-EPMC5445469 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature