title: CENCALC: a computational tool for conformational entropy calculations from molecular simulations.
abstract: We present the CENCALC software that has been designed to estimate the conformational entropy of single molecules from extended Molecular Dynamics (MD) simulations in the gas-phase or in solution. CENCALC uses both trajectory coordinates and topology information in order to characterize the conformational states of the molecule of interest by discretizing the time evolution of internal rotations. The implemented entropy methods are based on the mutual information expansion, which is built upon the converged probability density functions of the individual torsion angles, pairs of torsions, triads, and so on. Particularly, the correlation-corrected multibody local approximation selects an optimum cutoff in order to retrieve the maximum amount of genuine correlation from a given MD trajectory. We illustrate these capabilities by carrying out conformational entropy calculations for a decapeptide molecule either in its unbound form or in complex with a metalloprotease enzyme. CENCALC is distributed under the GNU public license at http://sourceforge.net/projects/cencalc/.
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA. esuarez@pitt.edu
authors.forename: Ernesto
authors.initials: E
authors.lastname: Suárez
authors.forename: Natalia
authors.initials: N
authors.lastname: Díaz
authors.forename: Jefferson
authors.initials: J
authors.lastname: Méndez
authors.forename: Dimas
authors.initials: D
authors.lastname: Suárez
mesh_terms: D000595:Amino Acid Sequence; D019277:Entropy; D006801:Humans; D020783:Matrix Metalloproteinase 7 / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D012984:Software
chemical_list: D010455:Peptides; D020783:Matrix Metalloproteinase 7