PDIviz: analysis and visualization of protein-DNA binding interfaces.

ABSTRACT:

Unlabelled

Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein-DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence. PDIviz allows for the generation of publication quality images, all calculated

SUBMITTER: Ribeiro J 

PROVIDER: S-EPMC4528634 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature