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

MOTIVATION

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.

RESULTS

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.

AVAILABILITY AND IMPLEMENTATION

Toolkit and documentation are freely available at http://sbcb.inf.ufrgs.br/confid.

CONTACT

marcelo.poleto@ufv.br or bigrisci@inf.ufrgs.br.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.