title: Free energy simulations come of age: protein-ligand recognition.
abstract: In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide an understanding of the interactions involved that goes beyond, and is an important complement to, experimental studies. Poisson-Boltzmann electrostatic models provide a faster and simpler free energy method in cases where electrostatic interactions are important. We illustrate both molecular dynamics and Poisson-Boltzmann methods with a detailed study of amino acid recognition by aspartyl-tRNA synthetase, whose specificity is important for maintaining the integrity of the genetic code.
authors.affiliation: Laboratoire de Biologie et G'enomique Structurales (CNRS), IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Strasbourg, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Simonson
authors.forename: Georgios
authors.initials: G
authors.lastname: Archontis
authors.forename: Martin
authors.initials: M
authors.lastname: Karplus
mesh_terms: D003198:Computer Simulation / Q000639:trends*; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins