ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories.

Abstract

The conformational space of small molecules can be vast and difficult to assess. Molecular dynamics (MD) simulations of free ligands in solution have been applied to predict conformational populations, but their characterization is often based on clustering algorithms or manual efforts. Here, we introduce ConfID, an analytical tool for conformational characterization of small molecules using MD trajectories. The evolution of conformational sampling and population frequencies throughout trajectories is calculated to check for sampling convergence while allowing to map relevant conformational transitions. The tool is designed to track conformational transition events and calculate time-dependent properties for each conformational population detected. Toolkit and documentation are freely available at http://sbcb.inf.ufrgs.br/confid. marcelo.poleto@ufv.br or bigrisci@inf.ufrgs.br. Supplementary data are available at Bioinformatics online.