Denis Navarro , Universidad de Zaragoza , Zaragoza
Oscar Lucia , University of Zaragoza, Zaragoza
Oscar Jiménez , Universidad de Zaragoza, Zaragoza
José M. Gil-Narvión , Instituto de Biocomputación y Física de Sistemas Complejos BIFI, Zaragoza
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/MCSE.2012.88
Virtual screening is a key process when developing a new drug in order to identify the most suitable molecule combinations. One of the most used direct computational method is molecule docking, based on analyzing the molecule structures in order to establish the affinity between them. This requires computing large databases in order to identify possible affinities between molecules, which allow reducing the initial database to an affordable size. In this paper, the special purpose FPGA-based JANUS supercomputer is used in order to accelerate the virtual screening process. The implemented docking algorithm is explained and the digital architecture is detailed. This design takes advantage of the paralleling possibilities of the computing problem, which perfectly fits the FPGA architecture.
Denis Navarro, Oscar Lucia, Oscar Jiménez, José M. Gil-Narvión, "FPGA-Based Virtual Screening Acceleration of Rigid-Molecule Docking", Computing in Science & Engineering, , no. 1, pp. , PrePrints PrePrints, doi:10.1109/MCSE.2012.88