title: Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.
abstract: Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein-ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein-ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein-ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.
authors.affiliation: Institut de Biologie Computationnelle, LIRMM, CNRS, Université de Montpellier, Montpellier 34095, France. daniel.roche@lirmm.fr.|Centre de Recherche de Biochimie Macromoléculaire, CNRS-UMR 5237, Montpellier 34293, France. daniel.roche@lirmm.fr.
authors.forename: Daniel Barry
authors.initials: DB
authors.lastname: Roche
authors.affiliation: School of Biological Sciences, University of Reading, Reading RG6 6AS, UK. d.a.brackenridge@pgr.reading.ac.uk.
authors.forename: Danielle Allison
authors.initials: DA
authors.lastname: Brackenridge
authors.affiliation: School of Biological Sciences, University of Reading, Reading RG6 6AS, UK. l.j.mcguffin@reading.ac.uk.
authors.forename: Liam James
authors.initials: LJ
authors.lastname: McGuffin
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D063990:Gene Ontology; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: binding-site residue prediction; biochemical functional elucidation; biological and biochemical role of enzymes; enzyme commission numbers; gene Ontology; protein function prediction; protein–ligand binding site prediction; sequence-based function prediction; structure-based function prediction