{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T10:40:09Z","timestamp":1748601609746,"version":"3.41.0"},"publisher-location":"Cham","reference-count":23,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319228846"},{"type":"electronic","value":"9783319228853"}],"license":[{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015]]},"DOI":"10.1007\/978-3-319-22885-3_29","type":"book-chapter","created":{"date-parts":[[2015,9,1]],"date-time":"2015-09-01T09:57:08Z","timestamp":1441101428000},"page":"336-350","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Exploiting the Parallel Execution of Homology Workflow Alternatives in HPC Compute Clouds"],"prefix":"10.1007","author":[{"given":"Kary A. C. S.","family":"Oca\u00f1a","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"de Oliveira","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"V\u00edtor","family":"Silva","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia","family":"Benza","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marta","family":"Mattoso","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,9,2]]},"reference":[{"key":"29_CR1","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1016\/j.drudis.2009.04.006","volume":"14","author":"CN Cavasotto","year":"2009","unstructured":"Cavasotto, C.N., Phatak, S.S.: Homology modeling in drug discovery: current trends and applications. Drug Discov. Today. 14, 676\u2013683 (2009)","journal-title":"Drug Discov. Today."},{"key":"29_CR2","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1109\/MC.2007.421","volume":"40","author":"Y Gil","year":"2007","unstructured":"Gil, Y., Deelman, E., Ellisman, M., Fahringer, T., Fox, G., Gannon, D., Goble, C., Livny, M., Moreau, L., Myers, J.: Examining the challenges of scientific workflows. Computer 40, 24\u201332 (2007)","journal-title":"Computer"},{"key":"29_CR3","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1109\/MCSE.2008.79","volume":"10","author":"J Freire","year":"2008","unstructured":"Freire, J., Koop, D., Santos, E., Silva, C.T.: Provenance for computational tasks: a survey. Comput. Sci. Eng. 10, 11\u201321 (2008)","journal-title":"Comput. Sci. Eng."},{"key":"29_CR4","unstructured":"Gil, Y., Ratnakar, V., Deelman, E., Mehta, G., Kim, J.: Wings for Pegasus: creating large-scale scientific applications using semantic representations of computational workflows. In: The National Conference on Artificial Intelligence, pp. 1767\u20131774, Vancouver, BC, Canada (2007)"},{"key":"29_CR5","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1007\/978-1-84628-757-2_23","volume-title":"Workflows for e-Science","author":"E Deelman","year":"2007","unstructured":"Deelman, E., Mehta, G., Singh, G., Su, M.-H., Vahi, K.: Pegasus: mapping large-scale workflows to distributed resources. In: Taylor, I.J., Deelman, E., Gannon, D.B., Shields, M. (eds.) Workflows for e-Science, pp. 376\u2013394. Springer, London (2007)"},{"key":"29_CR6","doi-asserted-by":"crossref","unstructured":"Santos, I., Dias, J., Oliveira, D., Ogasawara, E., Oca\u00f1a, K., Mattoso, M.: Runtime dynamic structural changes of scientific workflows in clouds. In: Proceedings of the IEEE\/ACM 6th International Workshop on Clouds and (eScience) Applications Management \u2013 CloudAM, pp. 417\u2013422. Dresden, Germany (2013)","DOI":"10.1109\/UCC.2013.83"},{"key":"29_CR7","doi-asserted-by":"crossref","unstructured":"Oliveira, D., Ogasawara, E., Bai\u00e3o, F., Mattoso, M.: SciCumulus: a lightweight cloud middleware to explore many task computing paradigm in scientific workflows. In: Proceedings of the 3rd International Conference on Cloud Computing, pp. 378\u2013385. IEEE, Washington, DC, USA (2010)","DOI":"10.1109\/CLOUD.2010.64"},{"key":"29_CR8","doi-asserted-by":"crossref","unstructured":"Costa, F., Silva, V., de Oliveira, D., Oca\u00f1a, K., Ogasawara, E., Dias, J., Mattoso, M.: Capturing and querying workflow runtime provenance with PROV: a practical approach. In: Proceedings of the Joint EDBT\/ICDT 2013 - Workshops on EDBT 2013, pp. 282\u2013289. ACM Press, NY, USA (2013)","DOI":"10.1145\/2457317.2457365"},{"key":"29_CR9","doi-asserted-by":"crossref","unstructured":"Moreau, L., Groth, P.: Provenance: an introduction to PROV. In: Synthesis Lectures on the Semantic Web: Theory and Technology, vol. 3(4), pp. 1-129. Morgan & Claypool Publishers, San Rafael (2013)","DOI":"10.2200\/S00528ED1V01Y201308WBE007"},{"key":"29_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2174\/157340910790980142","volume":"6","author":"F Shah","year":"2010","unstructured":"Shah, F., Mukherjee, P., Desai, P., Avery, M.: Computational approaches for the discovery of cysteine protease inhibitors against Malaria and SARS. Curr. Comput. Aided-Drug Des. 6, 1\u201323 (2010)","journal-title":"Curr. Comput. Aided-Drug Des."},{"key":"29_CR11","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1590\/S0036-46652009000500003","volume":"51","author":"JAL Lindoso","year":"2009","unstructured":"Lindoso, J.A.L., Lindoso, A.A.B.P.: Neglected tropical diseases in Brazil. Revista do Instituto de Medicina Tropical de S\u00e3o Paulo. 51, 247\u2013253 (2009)","journal-title":"Revista do Instituto de Medicina Tropical de S\u00e3o Paulo."},{"key":"29_CR12","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1007\/s10723-012-9227-2","volume":"10","author":"D Oliveira","year":"2012","unstructured":"Oliveira, D., Oca\u00f1a, K., Bai\u00e3o, F., Mattoso, M.: A provenance-based adaptive scheduling heuristic for parallel scientific workflows in clouds. J. Grid Comput. 10, 521\u2013552 (2012)","journal-title":"J. Grid Comput."},{"key":"29_CR13","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1146\/annurev.biophys.29.1.291","volume":"29","author":"MA Mart\u00ed-Renom","year":"2000","unstructured":"Mart\u00ed-Renom, M.A., Stuart, A.C., Fiser, A., S\u00e1nchez, R., Melo, F., Sali, A.: Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291\u2013325 (2000)","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"29_CR14","doi-asserted-by":"publisher","first-page":"D475","DOI":"10.1093\/nar\/gks1200","volume":"41","author":"PW Rose","year":"2013","unstructured":"Rose, P.W., Bi, C., Bluhm, W.F., Christie, C.H., Dimitropoulos, D., Dutta, S., Green, R.K., Goodsell, D.S., Prlic, A., Quesada, M., Quinn, G.B., Ramos, A.G., Westbrook, J.D., Young, J., Zardecki, C., Berman, H.M., Bourne, P.E.: The RCSB protein data bank: new resources for research and education. Nucleic Acids Res. 41, D475\u2013D482 (2013)","journal-title":"Nucleic Acids Res."},{"key":"29_CR15","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul, S.F., Madden, T.L., Sch\u00e4ffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389\u20133402 (1997)","journal-title":"Nucleic Acids Res."},{"key":"29_CR16","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1007\/978-1-60327-058-8_8","volume":"426","author":"N Eswar","year":"2008","unstructured":"Eswar, N., Eramian, D., Webb, B., Shen, M.-Y., Sali, A.: Protein structure modeling with MODELLER. Methods Mol. Biol. 426, 145\u2013159 (2008)","journal-title":"Methods Mol. Biol."},{"key":"29_CR17","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1093\/protein\/1.5.377","volume":"1","author":"MJ Sutcliffe","year":"1987","unstructured":"Sutcliffe, M.J., Haneef, I., Carney, D., Blundell, T.L.: Knowledge based modelling of homologous proteins, part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1, 377\u2013384 (1987)","journal-title":"Protein Eng."},{"key":"29_CR18","doi-asserted-by":"publisher","first-page":"956","DOI":"10.1002\/pro.5560060502","volume":"6","author":"H Li","year":"1997","unstructured":"Li, H., Tejero, R., Monleon, D., Bassolino-Klimas, D., Abate-Shen, C., Bruccoleri, R.E., Montelione, G.T.: Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1. Protein Sci. 6, 956\u2013970 (1997)","journal-title":"Protein Sci."},{"key":"29_CR19","volume-title":"Jackal: a Protein Structure Modeling Package","author":"JZ Xiang","year":"2002","unstructured":"Xiang, J.Z., Honig, B.: Jackal: a Protein Structure Modeling Package. Columbia University and Howard Hughes Medical Institute, New York (2002)"},{"key":"29_CR20","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1038\/nsb0295-163","volume":"2","author":"P Koehl","year":"1995","unstructured":"Koehl, P., Delarue, M.: A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling. Nat. Struct. Biol. 2, 163\u2013170 (1995)","journal-title":"Nat. Struct. Biol."},{"key":"29_CR21","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1107\/S0021889892009944","volume":"26","author":"RA Laskowski","year":"1993","unstructured":"Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M.: PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283\u2013291 (1993)","journal-title":"J. Appl. Crystallogr."},{"key":"29_CR22","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkn721","volume":"37","author":"KD Pruitt","year":"2009","unstructured":"Pruitt, K.D., Tatusova, T., Klimke, W., Maglott, D.R.: NCBI reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 37, D32\u2013D36 (2009)","journal-title":"Nucleic Acids Res."},{"key":"29_CR23","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1093\/bioinformatics\/bti770","volume":"22","author":"K Arnold","year":"2006","unstructured":"Arnold, K., Bordoli, L., Kopp, J., Schwede, T.: The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22, 195\u2013201 (2006)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Service-Oriented Computing - ICSOC 2014 Workshops"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-22885-3_29","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T10:08:38Z","timestamp":1748599718000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-319-22885-3_29"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9783319228846","9783319228853"],"references-count":23,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-22885-3_29","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2015]]},"assertion":[{"value":"2 September 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}