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Life science research and drug discovery at the turn of the 21st century: the experience of SwissBioGrid

Matthijs den Besten, Arthur J Thomas, Ralph Schroeder
2009 Journal of Biomedical Discovery and Collaboration  
SwissBioGrid gave rise to two pilot projects: one for proteomics data analysis and the other for high-throughput molecular docking ("virtual screening") to find new drugs for neglected diseases (specifically  ...  In 2004, a group of researchers in Switzerland established a project, SwissBioGrid, to explore whether Grid computing technologies could be successfully deployed within the life sciences.  ...  We also thank Michael Ashburner (University of Cambridge, Dept. of Genetics) and Graham Cameron (EBI) for their helpful insights on the problems of data management in the life sciences.  ... 
pmid:19521952 pmcid:PMC2850249 fatcat:6qnmmqkqkbfk3hevuluwfs2byu

Exploring Large Scale Receptor-Ligand Pairs in Molecular Docking Workflows in HPC Clouds

Kary Ocana, Silvia Benza, Daniel de Oliveira, Jonas Dias, Marta Mattoso
2014 2014 IEEE International Parallel & Distributed Processing Symposium Workshops  
We present SciDock, a molecular docking-based virtual screening workflow and evaluate its execution using 10,000 receptor-ligand pairs related to proteases enzymes of protozoan genomes.  ...  The overall performance of SciDock using 32 cores, in cloud virtual machines, reaches improvements up to 95.4% when running SciDock with AutoDock and 96.1% when running SciDock with Vina.  ...  We demonstrate that, using SciDock, it is possible to test in silico a set of receptors and ligands of interest for drug target candidates.  ... 
doi:10.1109/ipdpsw.2014.65 dblp:conf/ipps/OcanaBODM14 fatcat:am7be7jsfbbedlqtafsijs72dy

Distributed Computing in a Pandemic

Jamie Alnasir
2022 Advances in Distributed Computing and Artificial Intelligence Journal  
drug-repurposing, and high-throughput gene analysis -- and Sentinel, an XPE-Cray based system used to explore natural products.  ...  Grids and clouds both can also be used for international collaboration by enabling access to important datasets and providing services that allow researchers to focus on research rather than on time-consuming  ...  In the final in-silico docking phase, AutoDock Vina was run in parallel using an MPI wrapper.  ... 
doi:10.14201/adcaij.27337 fatcat:5dke4cbqnvcfhgaqymvfgj77xu

Distributed Computing in a Pandemic: A Review of Technologies Available for Tackling COVID-19 [article]

Jamie J Alnasir
2021 arXiv   pre-print
drug-repurposing, and high-throughput gene analysis -- and Sentinel, an XPE-Cray based system used to explore natural products.  ...  Grids and clouds both can also be used for international collaboration by enabling access to important datasets and providing services that allow researchers to focus on research rather than on time-consuming  ...  In the final in-silico docking phase, AutoDock Vina was run in parallel using an MPI wrapper.  ... 
arXiv:2010.04700v3 fatcat:kxakuqjlyjfilbroj5nl55xgbq

Cloud Computing in Healthcare and Biomedicine

Barbara Calabrese, Mario Cannataro
2015 Scalable Computing : Practice and Experience  
to the use of such platforms for the storage and analysis of patients data.  ...  High throughput platforms available in clinical settings or in research laboratories, such as magnetic resonance imaging, microarray, mass spectrometry and next-generation sequencing, are producing an  ...  AutoDockCloud [57] is a workflow system that enables distributed screening on a cloud platform using the molecular docking program AutoDock.  ... 
doi:10.12694/scpe.v16i1.1057 fatcat:k5s2o37zcrge5pvbwimhotbsca

Workflow-as-a-Service Cloud Platform and Deployment of Bioinformatics Workflow Applications [article]

Muhammad H. Hilman, Maria A. Rodriguez, Rajkumar Buyya
2020 arXiv   pre-print
Workflow management systems (WMS) support the composition and deployment of workflow-oriented applications in distributed computing environments.  ...  Based on this requirement, we extend CloudBus WMS functionality to handle the workload of multiple workflows and develop the WaaS cloud platform prototype.  ...  It is a prominent WMS and widely used for in silico experiments [7] [8] [9] .  ... 
arXiv:2006.01957v1 fatcat:z5paewg2mrgdxnkqvcsvu3gzmu

Developing science gateways for drug discovery in a grid environment

Horacio Pérez-Sánchez, Vahid Rezaei, Vitaliy Mezhuyev, Duhu Man, Jorge Peña-García, Helena den-Haan, Sandra Gesing
2016 SpringerPlus  
Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases.  ...  Results: To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific  ...  This work was partially supported by the Fundación Séneca del Centro de Investigación de la Región de Murcia under Project 18946/JLI/13 and by the Nils Coordinated Mobility under Grant 012ABELCM2014A, in  ... 
doi:10.1186/s40064-016-2914-x pmid:27547674 pmcid:PMC4978646 fatcat:oulkcqzd7zemdiagyo6bcencla

Building a virtual ligand screening pipeline using free software: a survey

Enrico Glaab
2015 Briefings in Bioinformatics  
He has set up and manages the Institute's virtual screening pipeline and works on drug target prioritization using omics data, screening based on receptors and ligands and biological applications of machine  ...  In this survey, an overview of recent developments in this field is presented, focusing on free software and data repositories for screening as alternatives to their commercial counterparts, and outlining  ...  Importantly, issues in data heterogeneity, redundancies and biases in the database curation process can result in biased in silico models of drug effects, and strategies proposed to address or alleviate  ... 
doi:10.1093/bib/bbv037 pmid:26094053 pmcid:PMC4793892 fatcat:jwhqn6n3hnh4pjtcmbgv4jq6ia

Computational Approaches to Identify a Hidden Pharmacological Potential in Large Chemical Libraries

2020 Supercomputing Frontiers and Innovations  
We also carried out virtual screening among one billion substances to find compounds potentially possessing anti-SARS-CoV-2 activity.  ...  These compounds belong to the chemical classes, in which the agonistic effect on TLR 7/8 had not been previously shown.  ...  which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is properly cited.  ... 
doi:10.14529/jsfi200306 fatcat:aiftubeld5czne7axlhrlxffoa

Applying high-performance computing in drug discovery and molecular simulation

Tingting Liu, Dong Lu, Hao Zhang, Mingyue Zheng, Huaiyu Yang, Yechun Xu, Cheng Luo, Weiliang Zhu, Kunqian Yu, Hualiang Jiang
2016 National Science Review  
This review mainly focuses on the application of HPC to the fields of drug discovery and molecular simulation at the Chinese Academy of Sciences, including virtual drug screening, molecular dynamics simulation  ...  This approach has yielded a series of new algorithms in drug design, as well as new software and databases.  ...  ACKNOWLEDGEMENTS We thank the SCCAS, the Shanghai Supercomputer Center, the National Supercomputer Center in Tianjin, and the National Supercomputer Center in Guangzhou for supporting our virtual screening  ... 
doi:10.1093/nsr/nww003 pmid:32288960 pmcid:PMC7107815 fatcat:bhur7mu3lfap5a4lhczgtrbmzm

Supercomputing Pipelines Search for Therapeutics Against COVID-19

Josh Vincent Vermaas, Ada Sedova, Matthew Baker, Swen Boehm, David Rogers, Jeff Larkin, Jens Glaser, Micholas Smith, Oscar Hernandez, Jeremy Smith
2020 Computing in science & engineering (Print)  
allow for the virtual screening of billions of potential drug compounds in days compared to weeks or months for their ability to inhibit SARS-COV-2 proteins.  ...  The urgent search for drugs to combat SARS-CoV-2 has included the use of supercomputers.  ...  , industry, and academic leaders who are volunteering free compute time and resources in support of COVID-19 research, and used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge  ... 
doi:10.1109/mcse.2020.3036540 pmid:35939280 pmcid:PMC9280802 fatcat:xazftle4uvgf3ndsk6ziaushyi

A Review on Parallel Virtual Screening Softwares for High-Performance Computers

Natarajan Arul Murugan, Artur Podobas, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Stefano Markidis
2022 Pharmaceuticals  
As the problem is to find the most stable (global) minima for numerous protein–ligand complexes (on the order of 106 to 1012), the parallel implementation of in silico virtual screening can be exploited  ...  Overall, drug discovery is a multivariable optimization and can be carried out in supercomputers using a reliable scoring function which is a measure of binding affinity or inhibition potential of the  ...  One of the most promising techniques to accelerate the drug discovery process, and to make it more cost-effective, is to perform in silico virtual screening, and to exploit the computational power of large  ... 
doi:10.3390/ph15010063 pmid:35056120 pmcid:PMC8780228 fatcat:t5e6d5kwt5hzzfkc7i5zxfj6re

Asia Federation Report on International Symposium on Grid Computing (ISGC) 2010 [chapter]

Francois Grey, Simon C. Lin
2011 Data Driven e-Science  
For example, South Korea's KISTI now leads development of AMGA, an official EGEE gLite middleware component for a metadata catalogue service on the grid.  ...  As EUAsiaGrid comes to a close in 2010, a key question, how to transition from Grids to a grid/cloud hybrid world. Finally, the issue of af-S.C. Lin and E.  ...  In vitro assay of compounds selected from in-silico screening performed at Academia Sinica.  ... 
doi:10.1007/978-1-4419-8014-4_1 fatcat:r426skzf5jbddeuvp6q3yfm3z4

Large-scale virtual screening for discovering leads in the postgenomic era

B. Waszkowycz, T. D. J. Perkins, R. A. Sykes, J. Li
2001 IBM Systems Journal  
This paper discusses the broader scope of virtual screening and, as an example, describes our recent work in docking one million compounds into the estrogen hormone receptor in order to highlight the technical  ...  The virtual screening technology of Protherics Molecular Design Ltd. is based on its integrated software environment for receptorbased drug design, called Prometheus.  ...  Acknowledgments For assistance with the modeling, programming, and administrative tasks involved in the DockCrunch project, we acknowledge the contributions of Carol Baxter, Chris Murray, Paul Greaney,  ... 
doi:10.1147/sj.402.0360 fatcat:dcnfx36lqffcro2lxcprhl4e5y

Some Critical Aspects of Molecular Interactions Between Drugs and Receptors

María J. R. Yunta
2014 American Journal of Modeling and Optimization  
Protonation states, for both proteins and drugs, need to be considered in docking studies although they have been usually neglected.  ...  This mini-review seeks to identify the importance of knowing the influence of pH in such studies to better achieve correct predictions for drug candidates.  ...  Until such a procedure is implemented, it is recommended to use only the standard protonation in docking and especially in virtual screening experiments.  ... 
doi:10.12691/ajmo-2-4-1 fatcat:2jbbqnqnvvhvjcfikm5jcjmjzq
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