wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model
Molecular docking simulations of fully flexible protein receptor (FFR) models are coming of age. In our studies, an FFR model is represented by a series of different conformations derived from a molecular dynamic simulation trajectory of the receptor. For each conformation in the FFR model, a dockin...
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ftpubmed:oai:pubmedcentral.nih.gov:3652109 2023-05-15T18:11:34+02:00 wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model De Paris, Renata Frantz, Fábio A. Norberto de Souza, Osmar Ruiz, Duncan D. A. 2013 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652109 http://www.ncbi.nlm.nih.gov/pubmed/23691504 https://doi.org/10.1155/2013/469363 en eng Hindawi Publishing Corporation http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652109 http://www.ncbi.nlm.nih.gov/pubmed/23691504 http://dx.doi.org/10.1155/2013/469363 Copyright © 2013 Renata De Paris et al. 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. CC-BY Methodology Report Text 2013 ftpubmed https://doi.org/10.1155/2013/469363 2013-09-04T23:39:48Z Molecular docking simulations of fully flexible protein receptor (FFR) models are coming of age. In our studies, an FFR model is represented by a series of different conformations derived from a molecular dynamic simulation trajectory of the receptor. For each conformation in the FFR model, a docking simulation is executed and analyzed. An important challenge is to perform virtual screening of millions of ligands using an FFR model in a sequential mode since it can become computationally very demanding. In this paper, we propose a cloud-based web environment, called web Flexible Receptor Docking Workflow (wFReDoW), which reduces the CPU time in the molecular docking simulations of FFR models to small molecules. It is based on the new workflow data pattern called self-adaptive multiple instances (P-SaMIs) and on a middleware built on Amazon EC2 instances. P-SaMI reduces the number of molecular docking simulations while the middleware speeds up the docking experiments using a High Performance Computing (HPC) environment on the cloud. The experimental results show a reduction in the total elapsed time of docking experiments and the quality of the new reduced receptor models produced by discarding the nonpromising conformations from an FFR model ruled by the P-SaMI data pattern. Text sami PubMed Central (PMC) BioMed Research International 2013 1 12 |
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Methodology Report De Paris, Renata Frantz, Fábio A. Norberto de Souza, Osmar Ruiz, Duncan D. A. wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model |
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Methodology Report |
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Molecular docking simulations of fully flexible protein receptor (FFR) models are coming of age. In our studies, an FFR model is represented by a series of different conformations derived from a molecular dynamic simulation trajectory of the receptor. For each conformation in the FFR model, a docking simulation is executed and analyzed. An important challenge is to perform virtual screening of millions of ligands using an FFR model in a sequential mode since it can become computationally very demanding. In this paper, we propose a cloud-based web environment, called web Flexible Receptor Docking Workflow (wFReDoW), which reduces the CPU time in the molecular docking simulations of FFR models to small molecules. It is based on the new workflow data pattern called self-adaptive multiple instances (P-SaMIs) and on a middleware built on Amazon EC2 instances. P-SaMI reduces the number of molecular docking simulations while the middleware speeds up the docking experiments using a High Performance Computing (HPC) environment on the cloud. The experimental results show a reduction in the total elapsed time of docking experiments and the quality of the new reduced receptor models produced by discarding the nonpromising conformations from an FFR model ruled by the P-SaMI data pattern. |
format |
Text |
author |
De Paris, Renata Frantz, Fábio A. Norberto de Souza, Osmar Ruiz, Duncan D. A. |
author_facet |
De Paris, Renata Frantz, Fábio A. Norberto de Souza, Osmar Ruiz, Duncan D. A. |
author_sort |
De Paris, Renata |
title |
wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model |
title_short |
wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model |
title_full |
wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model |
title_fullStr |
wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model |
title_full_unstemmed |
wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model |
title_sort |
wfredow: a cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model |
publisher |
Hindawi Publishing Corporation |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652109 http://www.ncbi.nlm.nih.gov/pubmed/23691504 https://doi.org/10.1155/2013/469363 |
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sami |
genre_facet |
sami |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652109 http://www.ncbi.nlm.nih.gov/pubmed/23691504 http://dx.doi.org/10.1155/2013/469363 |
op_rights |
Copyright © 2013 Renata De Paris et al. 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. |
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CC-BY |
op_doi |
https://doi.org/10.1155/2013/469363 |
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BioMed Research International |
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2013 |
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12 |
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1766184224877969408 |