Abstract
Molecular docking simulations of Fully-flexible Protein Receptor (FFR) models are coming of age. However, it demands High Performance Computing (HPC) for its executions and generates huge amounts of data that needs to be analyzed. Distributed HPC systems and scientific workflows are routinely applied to execute compute intensive tasks and to manage data flow. In this work we propose a conceptual Many Tasks Computing architecture to execute molecular docking simulations of FFR models to small molecules in distributed HPC environments.
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Coutinho, F., Ogasawara, E., de Oliveira, D., Braganholo, V., Lima, A.A.B., Dávila, A.M.R., Mattoso, M.: Data Parallelism in Bioinformatics Workflows Using Hydra. In: 19th ACM International Symposium on High Performance Distributed Computing, New York, pp. 507–515 (2010)
Luscombe, N.M., Greenbaum, D., Gerstein, M.: What is Bioinformatics? A Proposed Definition and Overview of the Field. Methods Inf. Med. 30, 346–358 (2001)
Kapetanovic, I.M.: Computer-aided drug discovery and development (CADD): In silico-chemico-biological approach. Chem. Biol. Interact. 17, 165–176 (2008)
Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S., Olson, A.J.: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791 (2009)
Machado, K.S., Winck, A.T., Ruiz, D.D.A., Norberto de Souza, O.: Mining flexible-receptor docking experiments to select promising protein receptor snapshots. BMC Genomics 11, 1–10 (2010)
Lin, J.H., Perryman, A.L., Schames, J.R., McCammom, J.A.: The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 68, 47–62 (2003)
Alonso, H., Bliznyuk, A.A., Gready, J.E.: Combining docking, molecular dynamic simulations in drug design. Med. Res. Rev. 26, 531–568 (2006)
Machado, K.S., Schroeder, E.K., Ruiz, D.D.A., Norberto de Souza, O.: Automating Molecular Docking with Explicit Receptor Flexibility Using Scientifc Workflow. In: Sagot, M.-F., Walter, M.E.M.T. (eds.) BSB 2007. LNCS (LNBI), vol. 4643, pp. 1–11. Springer, Heidelberg (2007)
Hübler, P.N.: P-SaMI: self-adapting multiple instances – a data pattern to scientific workflows (in portuguese: P-MIA: padrão de múltiplas instâncias autoadaptáveis – um padrão de dados para workflows científicos). PhD Thesis. PPGCC – PUCRS. Porto Alegre, RS, Brasil (2010)
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De Paris, R., Frantz, F.A., Norberto de Souza, O., Ruiz, D.D. (2011). A Conceptual Many Tasks Computing Architecture to Execute Molecular Docking Simulations of a Fully-Flexible Receptor Model. In: Norberto de Souza, O., Telles, G.P., Palakal, M. (eds) Advances in Bioinformatics and Computational Biology. BSB 2011. Lecture Notes in Computer Science(), vol 6832. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22825-4_11
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DOI: https://doi.org/10.1007/978-3-642-22825-4_11
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