CG2AA: backmapping protein coarse-grained structures.

MARCELO A MARTI; LUCIANA CAPECE; LEANDRO LOMBARDI

BIOINFORMATICS (OXFORD, ENGLAND)

OXFORD UNIV PRESS

Lugar: Oxford; Año: 2016

1367-4803

Summary: Coarse-grained (CG) models allow long-scale simulationswith a much lower computational cost than that of all-atom (AA)simulations. However, the absence of atomistic detail impedesthe analysis of specific atomic interactions that are determinant inmost interesting biomolecular processes. In order to study thesephenomena, it is necessary to reconstruct the atomistic structure fromthe CG representation. This structure can be analyzed by itself or beused as an onset for atomistic molecular dynamics simulations. In thiswork we present a computer program that accurately reconstructs theatomistic structure from CG models from the force field developedin (Hills et al., 2010), using a simple geometrical algorithm.Availability: The software is free and available online athttp://www.ic.fcen.uba.ar/cg2aa/cg2aa.pyContact: lula@qi.fcen.uba.arSupplementary information: More detail on the algorithm isavailable as online-only supplementary information at the journal?sweb site. Also, a tutorial and an example can be found athttp://www.ic.fcen.uba.ar/cg2aa/cg2aa.html