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Cloud Computing for Protein-Ligand Binding Site Comparison

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparis...

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Detalles Bibliográficos
Autores principales: Hung, Che-Lun, Hua, Guan-Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3671236/
https://www.ncbi.nlm.nih.gov/pubmed/23762824
http://dx.doi.org/10.1155/2013/170356
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author Hung, Che-Lun
Hua, Guan-Jie
author_facet Hung, Che-Lun
Hua, Guan-Jie
author_sort Hung, Che-Lun
collection PubMed
description The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.
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spelling pubmed-36712362013-06-12 Cloud Computing for Protein-Ligand Binding Site Comparison Hung, Che-Lun Hua, Guan-Jie Biomed Res Int Research Article The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery. Hindawi Publishing Corporation 2013 2013-05-16 /pmc/articles/PMC3671236/ /pubmed/23762824 http://dx.doi.org/10.1155/2013/170356 Text en Copyright © 2013 C.-L. Hung and G.-J. Hua. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Hung, Che-Lun
Hua, Guan-Jie
Cloud Computing for Protein-Ligand Binding Site Comparison
title Cloud Computing for Protein-Ligand Binding Site Comparison
title_full Cloud Computing for Protein-Ligand Binding Site Comparison
title_fullStr Cloud Computing for Protein-Ligand Binding Site Comparison
title_full_unstemmed Cloud Computing for Protein-Ligand Binding Site Comparison
title_short Cloud Computing for Protein-Ligand Binding Site Comparison
title_sort cloud computing for protein-ligand binding site comparison
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3671236/
https://www.ncbi.nlm.nih.gov/pubmed/23762824
http://dx.doi.org/10.1155/2013/170356
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