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

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. Howe...

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Detalles Bibliográficos
Autores principales: Roche, Daniel Barry, Brackenridge, Danielle Allison, McGuffin, Liam James
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691145/
https://www.ncbi.nlm.nih.gov/pubmed/26694353
http://dx.doi.org/10.3390/ijms161226202
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author Roche, Daniel Barry
Brackenridge, Danielle Allison
McGuffin, Liam James
author_facet Roche, Daniel Barry
Brackenridge, Danielle Allison
McGuffin, Liam James
author_sort Roche, Daniel Barry
collection PubMed
description 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.
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spelling pubmed-46911452016-01-06 Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods Roche, Daniel Barry Brackenridge, Danielle Allison McGuffin, Liam James Int J Mol Sci Review 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. MDPI 2015-12-15 /pmc/articles/PMC4691145/ /pubmed/26694353 http://dx.doi.org/10.3390/ijms161226202 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Roche, Daniel Barry
Brackenridge, Danielle Allison
McGuffin, Liam James
Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods
title Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods
title_full Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods
title_fullStr Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods
title_full_unstemmed Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods
title_short Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods
title_sort proteins and their interacting partners: an introduction to protein–ligand binding site prediction methods
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691145/
https://www.ncbi.nlm.nih.gov/pubmed/26694353
http://dx.doi.org/10.3390/ijms161226202
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