FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking

Authors

  • Marek Olšák
  • Jiří Filipovič
  • Martin Prokop

Keywords:

Molecular docking, acceleration, CUDA, AutoDock

Abstract

The AutoDock suite is widely used molecular docking software consisting of two main programs -- AutoGrid for precomputation of potential grid maps and AutoDock for docking into potential grid maps. In this paper, the acceleration of potential maps generation based on AutoGrid and its implementation called FastGrid is presented. The most computationally expensive algorithms are accelerated using GPU, the rest of algorithms run on CPU with asymptotically lower time complexity that has been obtained using more sophisticated data structures than in the original AutoGrid code. Moreover, the CPU implementation is parallelized to fully exploit computational power of machines that are equipped with more CPU cores than GPUs. Our implementation outperforms original AutoGrid more than 400x for large, but quite common molecules and sufficiently large grids.

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Author Biographies

Marek Olšák

Faculty of Informatics, Masaryk University
Botanicka 68a
602 00 Brno, Czech Republic

Jiří Filipovič

Faculty of Informatics, Masaryk University
Botanicka 68a
602 00 Brno, Czech Republic

Martin Prokop

National Centre for Biomolecular Research
Faculty of Science, Masarych University
Kotlařska 2
611 37 Brno, Czech Republic

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Published

2012-01-26

How to Cite

Olšák, M., Filipovič, J., & Prokop, M. (2012). FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking. COMPUTING AND INFORMATICS, 29(6+), 1325–1336. Retrieved from https://www.cai.sk/ojs/index.php/cai/article/view/146