PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures.

ABSTRACT: PDBMD2CD is a new web server capable of predicting circular dichroism (CD) spectra for multiple protein structures derived from molecular dynamics (MD) simulations, enabling predictions from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for each of these structures provided by the user. Using MD enables exploration of systems that cannot be monitored by direct experimentation. Validation of MD-derived data from these types of trajectories can be difficult via conventional structure-determining techniques such as crystallography or nuclear magnetic resonance spectroscopy. CD is an experimental technique that can provide protein structure information from such conditions. The website utilizes a much faster (minimum ∼1000×) and more accurate approa

SUBMITTER: Drew ED 

PROVIDER: S-EPMC7319452 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature