title: Implicit solvent methods for free energy estimation.
abstract: Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several computational approaches. The aim of this review is to give an overview of existing theories and methods to estimate solvent effects giving a specific focus on the category of implicit solvent models and their use in Molecular Dynamics. In many of these models, the solvent is considered as a continuum homogenous medium, while the solute can be represented at the atomic detail and at different levels of theory. Despite their degree of approximation, implicit methods are still widely employed due to their trade-off between accuracy and efficiency. Their derivation is rooted in the statistical mechanics and integral equations disciplines, some of the related details being provided here. Finally, methods that combine implicit solvent models and molecular dynamics simulation, are briefly described.
authors.affiliation: CONCEPT Lab, D3 Computation, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
authors.forename: Sergio
authors.initials: S
authors.lastname: Decherchi
authors.affiliation: Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Masetti
authors.affiliation: CONCEPT Lab, D3 Computation, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
authors.forename: Ivan
authors.initials: I
authors.lastname: Vyalov
authors.affiliation: CONCEPT Lab, D3 Computation, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy. Electronic address: walter.rocchia@iit.it.
authors.forename: Walter
authors.initials: W
authors.lastname: Rocchia
mesh_terms: D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D012995:Solubility; D012996:Solutions; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D012996:Solutions; D012997:Solvents
keywords: Continuum electrostatics; Generalized Born model; Implicit solvent models; Molecular dynamics; Poisson–Boltzmann equation