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Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

1
Institut de Biologie Computationnelle, LIRMM, CNRS, Université de Montpellier, Montpellier 34095, France
2
Centre de Recherche de Biochimie Macromoléculaire, CNRS-UMR 5237, Montpellier 34293, France
3
School of Biological Sciences, University of Reading, Reading RG6 6AS, UK
*
Author to whom correspondence should be addressed.
Academic Editors: Tatyana Karabencheva-Christova and Christo Z. Christov
Int. J. Mol. Sci. 2015, 16(12), 29829-29842; https://doi.org/10.3390/ijms161226202
Received: 20 September 2015 / Revised: 2 December 2015 / Accepted: 10 December 2015 / Published: 15 December 2015
(This article belongs to the Collection Proteins and Protein-Ligand Interactions)
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. View Full-Text
Keywords: protein–ligand binding site prediction; protein function prediction; binding-site residue prediction; biochemical functional elucidation; sequence-based function prediction; structure-based function prediction; biological and biochemical role of enzymes; gene Ontology; enzyme commission numbers protein–ligand binding site prediction; protein function prediction; binding-site residue prediction; biochemical functional elucidation; sequence-based function prediction; structure-based function prediction; biological and biochemical role of enzymes; gene Ontology; enzyme commission numbers
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Roche, D.B.; Brackenridge, D.A.; McGuffin, L.J. Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods. Int. J. Mol. Sci. 2015, 16, 29829-29842.

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