![](/images/graphics-bg.png)
wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model
Joint Authors
De Paris, Renata
Frantz, Fábio A.
Norberto de Souza, Osmar
Ruiz, Duncan D. A.
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-04-11
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
De Paris, Renata& Frantz, Fábio A.& Norberto de Souza, Osmar& Ruiz, Duncan D. A.. 2013. wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model. BioMed Research International،Vol. 2013, no. 2013, pp.1-12.
https://search.emarefa.net/detail/BIM-1004374
Modern Language Association (MLA)
De Paris, Renata…[et al.]. wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model. BioMed Research International No. 2013 (2013), pp.1-12.
https://search.emarefa.net/detail/BIM-1004374
American Medical Association (AMA)
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. BioMed Research International. 2013. Vol. 2013, no. 2013, pp.1-12.
https://search.emarefa.net/detail/BIM-1004374
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1004374