title: Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models.
abstract: The increasing trend in the recent literature on coarse grained (CG) models testifies their impact in the study of complex systems. However, the CG model landscape is variegated: even considering a given resolution level, the force fields are very heterogeneous and optimized with very different parametrization procedures. Along the road for standardization of CG models for biopolymers, here we describe a strategy to aid building and optimization of statistics based analytical force fields and its implementation in the software package AsParaGS (Assisted Parameterization platform for coarse Grained modelS). Our method is based on the use and optimization of analytical potentials, optimized by targeting internal variables statistical distributions by means of the combination of different algorithms (i.e., relative entropy driven stochastic exploration of the parameter space and iterative Boltzmann inversion). This allows designing a custom model that endows the force field terms with a physically sound meaning. Furthermore, the level of transferability and accuracy can be tuned through the choice of statistical data set composition. The method-illustrated by means of applications to helical polypeptides-also involves the analysis of two and three variable distributions, and allows handling issues related to the FF term correlations. AsParaGS is interfaced with general-purpose molecular dynamics codes and currently implements the "minimalist" subclass of CG models (i.e., one bead per amino acid, Cα based). Extensions to nucleic acids and different levels of coarse graining are in the course.
authors.affiliation: Center for Nanotechnology and Innovation @NEST, Istituto Italiano di Tecnologia , Piazza San Silvestro 12, 56127 Pisa, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Mereghetti
authors.affiliation: Center for Nanotechnology and Innovation @NEST, Istituto Italiano di Tecnologia , Piazza San Silvestro 12, 56127 Pisa, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Maccari
authors.affiliation: NEST, Istituto Nanoscienze - CNR and Scuola Normale Superiore , Piazza San Silvestro 12, 56127 Pisa, Italy.
authors.forename: Giulia Lia Beatrice
authors.initials: GL
authors.lastname: Spampinato
authors.affiliation: NEST, Istituto Nanoscienze - CNR and Scuola Normale Superiore , Piazza San Silvestro 12, 56127 Pisa, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Tozzini
mesh_terms: D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry / Q000378:metabolism*; D003198:Computer Simulation; D019277:Entropy; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D017433:Protein Structure, Secondary; D013269:Stochastic Processes
chemical_list: D001704:Biopolymers; D010455:Peptides