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Modelling of Protein Surface Using Parallel Heterogeneous Architectures

In: Mathematical Models in Biology

Author

Listed:
  • Daniele D’Agostino

    (Institute of Applied Mathematics and Information Technologies, National Research Council of Italy)

  • Andrea Clematis

    (Institute of Applied Mathematics and Information Technologies, National Research Council of Italy)

  • Emanuele Danovaro

    (Institute of Applied Mathematics and Information Technologies, National Research Council of Italy)

  • Ivan Merelli

    (Institute for Biomedical Technologies, National Research Council of Italy)

Abstract

A proper representation of protein surfaces is an important task in bioinformatics and biophysics. In a previous work we described a parallel workflow, based on the isosurface extraction and the CUDA architecture, able to produce high-resolution molecular surfaces based on the Van der Waals, Solvent Accessible, Richards-Connolly and Blobby definitions. In particular it is able to create surfaces composed by hundred millions triangles in less than 30 s using a Nvidia GTX 580, with speedup values up to 88. However in most application such number of triangles can be difficult to manage. In this paper we present an extension able to reduce the size of the surfaces by performing a simplification step, keeping however an high quality of the results. In particular the focus of the paper is on the efficient use of heterogeneous compute capabilities available on present workstations: the large surface produced using the CUDA device is progressively transferred and simplified on the host using the multicore CPU.

Suggested Citation

  • Daniele D’Agostino & Andrea Clematis & Emanuele Danovaro & Ivan Merelli, 2015. "Modelling of Protein Surface Using Parallel Heterogeneous Architectures," Springer Books, in: Valeria Zazzu & Maria Brigida Ferraro & Mario R. Guarracino (ed.), Mathematical Models in Biology, edition 1, pages 189-199, Springer.
    • Handle: RePEc:spr:sprchp:978-3-319-23497-7_14
    DOI: 10.1007/978-3-319-23497-7_14
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