title: Modelling and enhanced molecular dynamics to steer structure-based drug discovery.
abstract: The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes.
authors.affiliation: Department of Computer Science and Computer Engineering, Faculty of Science, Technology and Engineering, La Trobe University, Melbourne, VIC 3086, Australia.
authors.forename: Subha
authors.initials: S
authors.lastname: Kalyaanamoorthy
authors.affiliation: Department of Computer Science and Computer Engineering, Faculty of Science, Technology and Engineering, La Trobe University, Melbourne, VIC 3086, Australia. Electronic address: phoebe.chen@latrobe.edu.au.
authors.forename: Yi-Ping Phoebe
authors.initials: YP
authors.lastname: Chen
mesh_terms: D000595:Amino Acid Sequence; D055808:Drug Discovery / Q000379:methods*; D006801:Humans; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009068:Movement; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics
chemical_list: D043562:Receptors, G-Protein-Coupled
keywords: Enhanced sampling molecular dynamics; Modelling; Molecular dynamics; Structure based drug discovery