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Multi-server approach for high-throughput molecular descriptors calculation based on multi-linear algebraic maps

dc.creatorGarcía-Jacas C.R.
dc.creatorAguilera-Mendoza L.
dc.creatorGonzález-Pérez R.
dc.creatorMarrero-Ponce Y.
dc.creatorAcevedo-Martínez L.
dc.creatorBarigye S.J.
dc.creatorAvdeenko T.
dc.date.accessioned2020-03-26T16:32:48Z
dc.date.available2020-03-26T16:32:48Z
dc.date.issued2015
dc.identifier.citationMolecular Informatics; Vol. 34, Núm. 1; pp. 60-69
dc.identifier.issn18681743
dc.identifier.urihttps://hdl.handle.net/20.500.12585/9031
dc.description.abstractThe present report introduces a novel module of the QuBiLS-MIDAS software for the distributed computation of the 3D Multi-Linear algebraic molecular indices. The main motivation for developing this module is to deal with the computational complexity experienced during the calculation of the descriptors over large datasets. To accomplish this task, a multi-server computing platform named Tarenal was developed, which is suited for institutions with many workstations interconnected through a local network and without resources particularly destined for computation tasks. This new system was deployed in 337 workstations and it was perfectly integrated with the QuBiLSMIDAS software. To illustrate the usability of the T-arenal platform, performance tests over a dataset comprised of 15000 compounds are carried out, yielding a 52 and 60 fold reduction in the sequential processing time for the 2-Linear and 3-Linear indices, respectively. Therefore, it can be stated that the T-arenal based distribution of computation tasks constitutes a suitable strategy for performing high-throughput calculations of 3D Multi-Linear descriptors over thousands of chemical structures for posterior QSAR and/or ADME-Tox studies. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.eng
dc.format.mediumRecurso electrónico
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.publisherWiley-VCH Verlag
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.sourcehttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84921050627&doi=10.1002%2fminf.201400086&partnerID=40&md5=657413650a04d6f20e9d1896f3671f51
dc.titleMulti-server approach for high-throughput molecular descriptors calculation based on multi-linear algebraic maps
dcterms.bibliographicCitationBrown, F.K., (1998) Annu. Rep. Med. Chem., 33, pp. 375-384
dcterms.bibliographicCitationEngel, T., (2006) J. Chem. Inf. Comput. Sci., 46, pp. 2267-2277
dcterms.bibliographicCitationTodeschini, R., Consonni, V., (2009) Molecular Descriptors for Chemoinformatics, 1. , 1edst edWILEY-VCH, Weinheim
dcterms.bibliographicCitation(2010) DRAGON, V 6.0, , Milano Chemometrics and QSAR Research Group, Milano, Italy
dcterms.bibliographicCitationHong, H., Xie, Q., Ge, W., Qian, F., Fang, H., Shi, L., Su, Z., Tong, W., (2008) J. Chem. Inf. Comput. Sci., 48, pp. 1337-1344
dcterms.bibliographicCitation(2008) BlueDesk, , University of Tübingen, Tübingen, Germany
dcterms.bibliographicCitationLiu, K., Feng, J., Young, S.S., (2005) J. Chem. Inf. Model., 45, pp. 515-522
dcterms.bibliographicCitationYap, C.W., (2011) J. Comput. Chem., 32, pp. 1466-1474
dcterms.bibliographicCitationCODESSA III, , Semichen, Shawnee, USA
dcterms.bibliographicCitationADRIANA.Code, , Molecular Networks GmbH, Erlangen, Germany
dcterms.bibliographicCitation(2002) MODESLAB, V1.5, , MODesLab.com
dcterms.bibliographicCitationMolconn-Z, V4.10, , Hall Associates Consulting - Molconn.com, Quincy, MA, USA
dcterms.bibliographicCitationGuha, R., CDK Descriptor Calculator GUI, V1.3.9
dcterms.bibliographicCitationGarcía-Jacas, C.R., Marrero-Ponce, Y., Acevedo-Martínez, L., Barigye, S.J., Valdés-Martiní, J.R., Contreras-Torres, E., (2014) J. Comput. Chem., 35, pp. 1395-1409
dcterms.bibliographicCitationGarcía-Jacas, C.R., Marrero-Ponce, Y., Barigye, S.J., Valdés-Martiní, J.R., Rivera-Borroto, O.M., Verbel, J.O., (2014) Curr. Drug Metab., 15, pp. 441-469
dcterms.bibliographicCitationMarrero-Ponce, Y., García-Jacas, C.R., Barigye, S.J., Valdés-Martiní, J.R., Rivera-Borroto, O.M., Pino-Urias, R.W., Cubillán, N., Alvarado, Y.J., (2014) Curr. Bioinf., , in press
dcterms.bibliographicCitationGodden, J.W., Stahura, F.L., Bajorath, J., (2000) J. Chem. Inf. Comput. Sci., 40, pp. 796-800
dcterms.bibliographicCitationMardia, K.V., Kent, J.T., Bibby, J.M., (1979) Multivariate Analysis, , Academic Press, London
dcterms.bibliographicCitationSutherland, J.J., O'Brien, L.A., Weaver, D.F., (2004) J. Med. Chem., 47, pp. 5541-5554
dcterms.bibliographicCitationBonachéra, F., Horvath, D., (2008) J. Chem. Inf. Model., 48, pp. 409-425
dcterms.bibliographicCitationTosco, P., Balle, T., (2011) J. Chem. Inf. Model., 52, pp. 302-307
dcterms.bibliographicCitationHinselmann, G., Rosenbaum, L., Jahn, A., Fechner, N., Zell, A., (2011) J. Cheminf., 3, p. 3
dcterms.bibliographicCitationKlamt, A., Thormann, M., Wichmann, K., Tosco, P., (2012) J. Chem. Inf. Model., 52, pp. 2157-2164
dcterms.bibliographicCitationAnderson, D.P., (2004) Proc. Fifth IEEE/ACM Int. Workshop on Grid Computing, pp. 4-10. , IEEE
dcterms.bibliographicCitationAnderson, D.P., Korpela, E., Walton, R., (2005) First Int. Conf. e-Science and Grid Computing, pp. 203-211. , IEEE, Melbourne, Vic
dcterms.bibliographicCitationCirne, W., Brasileiro, F., Andrade, N., Costa, L., Andrade, A., Novaes, R., Mowbray, M., (2006) J Grid Comp., 4, pp. 225-246
dcterms.bibliographicCitationLam, C., (2010) Hadoop in Action, , Manning Publications Co., Greenwich, CT, USA
dcterms.bibliographicCitationKeane, T., Allen, R., Naughton, T.J., McInerney, J., Waldron, J., (2003) Scientific Engineering for Distributed Java Applications, 2604, pp. 122-131. , Eds: N. Guelfi, E. Astesiano, G. Reggio, Springer, Heidelberg
dcterms.bibliographicCitationKeane, T., (2004), Thesis, National University of Ireland Maynooth
dcterms.bibliographicCitationMarosi, A., Gombas, G., Balaton, Z., Kacsuk, P., Kiss, T., (2008) Making Grids Work, pp. 365-376. , Springer, US
dcterms.bibliographicCitationLitzkow, M.J., Livny, M., Mutka, M.W., 8th Int. Conf. Distributed Comp. Syst. IEEE, San Jose, CA, 1988, pp. 104-111
dcterms.bibliographicCitationNeary, M., Phipps, A., Richman, S., Cappello, P., (2000) Euro-Par 2000 Parallel Processing, 1900, pp. 1231-1238. , Eds: A. Bode, T. Ludwig, W. Karl, R. Wism-ller, Springer, Heidelberg
dcterms.bibliographicCitationFedak, G., Germain, C., Neri, V., Cappello, F., (2001) Proc. First IEEE/ACM Int. Symp. Cluster Computing and the Grid, pp. 582-587. , IEEE, Brisbane, Qld
dcterms.bibliographicCitationDomingues, P., Marques, P., Silva, L., (2005) Int. Conf. Workshops on Parallel Processing, pp. 469-476. , IEEE
dcterms.bibliographicCitationKondo, D., Taufer, M., Brooks, C., Casanova, H., Chien, A., (2004) Proc. 18th Int. Symp. Parallel Distributed Processing, p. 26. , IEEE
dcterms.bibliographicCitationKeane, T.M., Naughton, T.J., (2005) Bioinformatics, 21, pp. 1705-1706
dcterms.bibliographicCitationKeane, T.M., Naughton, T.J., Travers, S.A., McInerney, J.O., McCormack, G., (2005) Bioinformatics, 20, pp. 969-974
dcterms.bibliographicCitationPage, A., Keane, T., Allen, R., Naughton, T.J., Waldron, J., (2003) Proc. 2nd Int. Conf. Principles and Practice of Programming in Java, pp. 191-194. , Computer Science Press, Inc., Kilkenny City, Ireland
dcterms.bibliographicCitationLivny, M., Melman, M., (1982) SIGMETRICS Perform. Eval. Rev., 11, pp. 47-55
dcterms.bibliographicCitationPitt, E., McNiff, K., (2001) Java.Rmi: The Remote Method Invocation Guide, , Addison-Wesley Longman, Boston, MA, USA
datacite.rightshttp://purl.org/coar/access_right/c_16ec
oaire.resourceTypehttp://purl.org/coar/resource_type/c_6501
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.driverinfo:eu-repo/semantics/article
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1002/minf.201400086
dc.subject.keywords3D N-linear algebraic descriptors
dc.subject.keywordsDistributed computing system
dc.subject.keywordsMulti-server architecture
dc.subject.keywordsPlatform of distributed tasks
dc.subject.keywordsQuBiLS-MIDAS
dc.subject.keywordsT-arenal
dc.subject.keywordsTOMOCOMD-CARDD
dc.subject.keywordsAlgorithm
dc.subject.keywordsArticle
dc.subject.keywordsCalculation
dc.subject.keywordsChemical structure
dc.subject.keywordsCommunication protocol
dc.subject.keywordsMathematics
dc.subject.keywordsPerformance
dc.subject.keywordsPriority journal
dc.subject.keywordsQuantitative structure activity relation
dc.subject.keywordsSoftware
dc.subject.keywordsTheoretical model
dc.subject.keywordsModels, Theoretical
dc.subject.keywordsSoftware
dc.rights.accessRightsinfo:eu-repo/semantics/restrictedAccess
dc.rights.ccAtribución-NoComercial 4.0 Internacional
dc.identifier.instnameUniversidad Tecnológica de Bolívar
dc.identifier.reponameRepositorio UTB
dc.type.spaArtículo
dc.identifier.orcid56189852800
dc.identifier.orcid56035076700
dc.identifier.orcid56482981200
dc.identifier.orcid55665599200
dc.identifier.orcid56483284000
dc.identifier.orcid55363486500
dc.identifier.orcid6508351205


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