MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
Autor(a) principal: | |
---|---|
Data de Publicação: | 2010 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10198/3040 |
Resumo: | Background: Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. Implementation: MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. Conclusion: MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multiplatform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina. |
id |
RCAP_5ee3c225f93a5ce6b312ebe76492c52f |
---|---|
oai_identifier_str |
oai:bibliotecadigital.ipb.pt:10198/3040 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
|
spelling |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clustersBackground: Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. Implementation: MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. Conclusion: MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multiplatform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.Biblioteca Digital do IPBAbreu, Rui M.V.Froufe, Hugo J.C.Queiroz, Maria João R.P.Ferreira, Isabel C.F.R.2011-01-06T17:14:08Z20102010-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10198/3040engAbreu, Rui M.V.; Froufe, Hugo J.C.; Queiroz, Maria João R.P.; Ferreira, Isabel C.F.R. (2010). MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters. Journal of Cheminformatics. ISSN 1758-2946. 2:1, p. 101758-294610.1186/1758-2946-2-10info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-01-16T12:06:33ZPortal AgregadorONG |
dc.title.none.fl_str_mv |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters |
title |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters |
spellingShingle |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters Abreu, Rui M.V. |
title_short |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters |
title_full |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters |
title_fullStr |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters |
title_full_unstemmed |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters |
title_sort |
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters |
author |
Abreu, Rui M.V. |
author_facet |
Abreu, Rui M.V. Froufe, Hugo J.C. Queiroz, Maria João R.P. Ferreira, Isabel C.F.R. |
author_role |
author |
author2 |
Froufe, Hugo J.C. Queiroz, Maria João R.P. Ferreira, Isabel C.F.R. |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Biblioteca Digital do IPB |
dc.contributor.author.fl_str_mv |
Abreu, Rui M.V. Froufe, Hugo J.C. Queiroz, Maria João R.P. Ferreira, Isabel C.F.R. |
description |
Background: Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. Implementation: MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. Conclusion: MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multiplatform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina. |
publishDate |
2010 |
dc.date.none.fl_str_mv |
2010 2010-01-01T00:00:00Z 2011-01-06T17:14:08Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10198/3040 |
url |
http://hdl.handle.net/10198/3040 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Abreu, Rui M.V.; Froufe, Hugo J.C.; Queiroz, Maria João R.P.; Ferreira, Isabel C.F.R. (2010). MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters. Journal of Cheminformatics. ISSN 1758-2946. 2:1, p. 10 1758-2946 10.1186/1758-2946-2-10 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
|
repository.mail.fl_str_mv |
|
_version_ |
1777301804583747584 |