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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2013
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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. |
format | Online Article Text |
id | pubmed-3671236 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT hungchelun cloudcomputingforproteinligandbindingsitecomparison AT huaguanjie cloudcomputingforproteinligandbindingsitecomparison |