High throughput molecular dynamics for drug discovery

Molecular dynamics simulations hold the promise to be an important tool for biological research and drug discovery. Historically, however, there were several obstacles for it to become a practical research tool. Limitations in computer hardware had previously made it difficult to simulate for long e...

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Authors: Stanley, Nathaniel H., 1983-, De Fabritiis, Gianni
Format: article
Status:Published version
Publication Date:2015
Country:España
Institution:Universitat Pompeu Fabra
Repository:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/23279
Online Access:http://hdl.handle.net/10230/23279
http://dx.doi.org/10.1186/s40203-015-0007-0
Access Level:Open access
Keyword:Dinàmica molecular -- Simulació per ordinador
Drogues -- Anàlisi
High-throughput molecular dynamics
Markov state models
GPU
Drug discovery
Fragments
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spelling High throughput molecular dynamics for drug discoveryStanley, Nathaniel H., 1983-De Fabritiis, GianniDinàmica molecular -- Simulació per ordinadorDrogues -- AnàlisiHigh-throughput molecular dynamicsMarkov state modelsGPUDrug discoveryFragmentsMolecular dynamics simulations hold the promise to be an important tool for biological research and drug discovery. Historically, however, there were several obstacles for it to become a practical research tool. Limitations in computer hardware had previously made it difficult to simulate for long enough to see interesting biological processes. Recent improvements in hardware and algorithms have largely removed this issue, leaving data analysis as the main obstacle. Advances in Markov state modeling appear to be on the way to remove this obstacle. We outline these advances here and discuss numerous recent studies that demonstrate that molecular dynamics simulations will start to be an important tool for pharmaceutical research.SpringerOpen201520152015info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/23279http://dx.doi.org/10.1186/s40203-015-0007-0reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésIn Silico Pharmacology. 2015; 3: 3.© 2015 Stanley and De Fabritiis; licensee Springer. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.http://creativecommons.org/licenses/by/4.0info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/232792026-06-12T07:21:37Z
dc.title.none.fl_str_mv High throughput molecular dynamics for drug discovery
title High throughput molecular dynamics for drug discovery
spellingShingle High throughput molecular dynamics for drug discovery
Stanley, Nathaniel H., 1983-
Dinàmica molecular -- Simulació per ordinador
Drogues -- Anàlisi
High-throughput molecular dynamics
Markov state models
GPU
Drug discovery
Fragments
title_short High throughput molecular dynamics for drug discovery
title_full High throughput molecular dynamics for drug discovery
title_fullStr High throughput molecular dynamics for drug discovery
title_full_unstemmed High throughput molecular dynamics for drug discovery
title_sort High throughput molecular dynamics for drug discovery
dc.creator.none.fl_str_mv Stanley, Nathaniel H., 1983-
De Fabritiis, Gianni
author Stanley, Nathaniel H., 1983-
author_facet Stanley, Nathaniel H., 1983-
De Fabritiis, Gianni
author_role author
author2 De Fabritiis, Gianni
author2_role author
dc.subject.none.fl_str_mv Dinàmica molecular -- Simulació per ordinador
Drogues -- Anàlisi
High-throughput molecular dynamics
Markov state models
GPU
Drug discovery
Fragments
topic Dinàmica molecular -- Simulació per ordinador
Drogues -- Anàlisi
High-throughput molecular dynamics
Markov state models
GPU
Drug discovery
Fragments
description Molecular dynamics simulations hold the promise to be an important tool for biological research and drug discovery. Historically, however, there were several obstacles for it to become a practical research tool. Limitations in computer hardware had previously made it difficult to simulate for long enough to see interesting biological processes. Recent improvements in hardware and algorithms have largely removed this issue, leaving data analysis as the main obstacle. Advances in Markov state modeling appear to be on the way to remove this obstacle. We outline these advances here and discuss numerous recent studies that demonstrate that molecular dynamics simulations will start to be an important tool for pharmaceutical research.
publishDate 2015
dc.date.none.fl_str_mv 2015
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/23279
http://dx.doi.org/10.1186/s40203-015-0007-0
url http://hdl.handle.net/10230/23279
http://dx.doi.org/10.1186/s40203-015-0007-0
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv In Silico Pharmacology. 2015; 3: 3.
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv SpringerOpen
publisher.none.fl_str_mv SpringerOpen
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.811543

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