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5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011) pp 63–69Cite as

Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs

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Part of the book series: Advances in Intelligent and Soft Computing ((AINSC,volume 93))

Abstract

In this work we discuss the benefits of using massively parallel architectures for the optimization of Virtual Screeningmethods.We empirically demonstrate that GPUs are well suited architecture for the acceleration of non-bonded interaction kernels, obtaining up to a 260 times sustained speedup compared to its sequential counterpart version.

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References

  1. Harvey, M.J., De Fabritiis, G.: An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. J. Chem. Theory. Comput. 5, 2371–2377 (2009)

    Article  Google Scholar 

  2. Kokh, D., Wenzel, W.: Flexible side chain models improve enrichment rates in in silico screening. J. Med. Chem. 51, 5919–5931 (2008)

    Article  Google Scholar 

  3. NVIDIA. CUDA Programming Guide 3.2 (2010)

    Google Scholar 

  4. Pérez-Sánchez, H.E., Wenzel, W.: Implementation of an effective non-bonded interactions kernel for biomolecular simulations on the cell processor. In: Gesellschaft fuer Informatik, Jahrestagung 2009. LNI, vol. 154, pp. 721–729 (2009)

    Google Scholar 

  5. Pérez-Sánchez, H.E., Wenzel, W.: Optimization methods for virtual screening on novel computational architectures. Curr. Comput. Aided. Drug. Des. 7, 1–17 (2011)

    Article  Google Scholar 

  6. Pham, D., Aipperspach, T., Boerstler, D., Bolliger, M., Chaudhry, R., Cox, D., Harvey, P., Hofstee, H., Johns, C.: Overview of the architecture, circuit design, and physical implementation of a first-generation cell processor. IEEE J. Solid-State Circuits 41, 179–196 (2006)

    Article  Google Scholar 

  7. Schiller, A., Sutmann, G., Yang, L.: A Fast Wavelet Based Implementation to Calculate Coulomb Potentials on the Cell/B.E. In: Proceedings of the 2008 10th IEEE ICHPCC, pp. 162–168. IEEE Computer Society, Los Alamitos (2008)

    Google Scholar 

  8. Stone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G., Schulten, K.: Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 28, 2618–2640 (2007)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Grupo de Arquitectura y Computación Paralela, Dpto. de Ing. y Tecnología de Computadores Facultad de Informática, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain

    Ginés D. Guerrero, José M. Cecilia & José M. García

  2. Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany

    Horacio Pérez-Sánchez & Wolfgang Wenzel

Authors
  1. Ginés D. Guerrero
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  2. Horacio Pérez-Sánchez
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  3. Wolfgang Wenzel
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  4. José M. Cecilia
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  5. José M. García
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Editor information

Editors and Affiliations

  1. Dep. Informática / CCTC, Universidade do Minho, 4710 - 057, Braga, Portugal

    Miguel P. Rocha

  2. Department of Computing Science and Control Faculty of Science, University of Salamanca, Plaza de la Merced S/N, 37008, Salamanca, Spain

    Juan M. Corchado Rodríguez

  3. Edificio Politécnico, ESEI: Escuela Superior de Ingeniería Informática, 32004, Ourense, Spain

    Florentino Fdez-Riverola

  4. Structural Biology and BioComputing Programme (CNIO), Spanish National Cancer Research Centre, Melchor Fdez Almagro 3, 28029, Madrid, Spain

    Alfonso Valencia

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© 2011 Springer-Verlag Berlin Heidelberg

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Guerrero, G.D., Pérez-Sánchez, H., Wenzel, W., Cecilia, J.M., García, J.M. (2011). Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs. In: Rocha, M.P., Rodríguez, J.M.C., Fdez-Riverola, F., Valencia, A. (eds) 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Advances in Intelligent and Soft Computing, vol 93. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19914-1_9

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  • DOI: https://doi.org/10.1007/978-3-642-19914-1_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-19913-4

  • Online ISBN: 978-3-642-19914-1

  • eBook Packages: EngineeringEngineering (R0)

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