Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: De Paris, Renata, Frantz, Fábio A., Norberto de Souza, Osmar, Ruiz, Duncan D. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652109/
https://www.ncbi.nlm.nih.gov/pubmed/23691504
http://dx.doi.org/10.1155/2013/469363
_version_ 1782269276121464832
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
collection PubMed
description 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 Online
Article
Text
id pubmed-3652109
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Hindawi Publishing Corporation
record_format MEDLINE/PubMed
spelling pubmed-36521092013-05-20 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. Biomed Res Int Methodology Report 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. Hindawi Publishing Corporation 2013 2013-04-11 /pmc/articles/PMC3652109/ /pubmed/23691504 http://dx.doi.org/10.1155/2013/469363 Text en Copyright © 2013 Renata De Paris et al. 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 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
title 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_short 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
topic Methodology Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652109/
https://www.ncbi.nlm.nih.gov/pubmed/23691504
http://dx.doi.org/10.1155/2013/469363
work_keys_str_mv AT deparisrenata wfredowacloudbasedwebenvironmenttohandlemoleculardockingsimulationsofafullyflexiblereceptormodel
AT frantzfabioa wfredowacloudbasedwebenvironmenttohandlemoleculardockingsimulationsofafullyflexiblereceptormodel
AT norbertodesouzaosmar wfredowacloudbasedwebenvironmenttohandlemoleculardockingsimulationsofafullyflexiblereceptormodel
AT ruizduncanda wfredowacloudbasedwebenvironmenttohandlemoleculardockingsimulationsofafullyflexiblereceptormodel