JEDi: java essential dynamics inspector - a molecular trajectory analysis toolkit.

ABSTRACT:

Background

Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized software to facilitate workflows and analysis of molecular dynamics simulation data to fully harness the power of PCA is lacking. The Java Essential Dynamics inspector (JEDi) software is a major upgrade from the previous JED software.

Results

Employing multi-threading, JEDi features a user-friendly interface to control rapid workflows for interrogating conformational motions of biopolymers at various spatial resolutions and within subregions, including multiple chain proteins. JEDi has options for Cartesian-based coordinates (cPCA) and

SUBMITTER: David CC 

PROVIDER: S-EPMC8088583 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature