title: Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies.
abstract: Kinetic and thermodynamic ligand-protein binding parameters are gaining growing importance as key information to consider in drug discovery. The determination of the molecular structures, using particularly x-ray and NMR techniques, is crucial for understanding how a ligand recognizes its target in the final binding complex. However, for a better understanding of the recognition processes, experimental studies of ligand-protein interactions are needed. Even though several techniques can be used to investigate both thermodynamic and kinetic profiles for a ligand-protein complex, these procedures are very often laborious, time consuming and expensive. In the last 10 years, computational approaches have enormous potential in providing insights into each of the above effects and in parsing their contributions to the changes in both kinetic and thermodynamic binding parameters. The main purpose of this review is to summarize the state of the art of computational strategies for estimating the kinetic and thermodynamic parameters of a ligand-protein binding.
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical & Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Deganutti
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical & Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Moro
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D055808:Drug Discovery; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011506:Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins
keywords: kinetic ligand–protein binding parameters; ligand–protein recognition; molecular dynamics; molecular modeling; thermodynamic ligand–protein binding parameters