title: Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.
abstract: The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given.
authors: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland.
authors: Sereina
authors: S
authors: Riniker
authors: Clara D
authors: CD
authors: Christ
authors: Halvor S
authors: HS
authors: Hansen
authors: Philippe H
authors: PH
authors: Hünenberger
authors: Chris
authors: C
authors: Oostenbrink
authors: Denise
authors: D
authors: Steiner
authors: Wilfred F
authors: WF
authors: van Gunsteren
mesh_terms: D008024:Ligands; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D012984:Software; D013816:Thermodynamics
chemical_list: D008024:Ligands; D010455:Peptides