Cargando…
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...
Autores principales: | , , |
---|---|
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 |
_version_ | 1782407110320979968 |
---|---|
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. |
format | Online Article Text |
id | pubmed-4691145 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT rochedanielbarry proteinsandtheirinteractingpartnersanintroductiontoproteinligandbindingsitepredictionmethods AT brackenridgedanielleallison proteinsandtheirinteractingpartnersanintroductiontoproteinligandbindingsitepredictionmethods AT mcguffinliamjames proteinsandtheirinteractingpartnersanintroductiontoproteinligandbindingsitepredictionmethods |