Current Drug Targets

Francis J. Castellino
Kleiderer-Pezold Professor of Biochemistry
Director, W.M. Keck Center for Transgene Research
Dean Emeritus, College of Science
230 Raclin-Carmichael Hall, University of Notre Dame
Notre Dame, IN 46556
USA

Back

Translate in Chinese

Structure-Based Drug Discovery Accelerated by Many-Core Devices

Author(s): Wei Feinstein, Michal Brylinski.

Graphical Abstract:


Abstract:

Computer-aided design is one of the critical components of modern drug discovery. Drug development is routinely streamlined using computational approaches to improve hit identification and lead selection, enhance bioavailability, and reduce toxicity. A mounting body of genomic knowledge accumulated during the last decade or so presents great opportunities for pharmaceutical research. However, new challenges also arose because processing this large volume of data demands unprecedented computing resources. On the other hand, the state-of-the-art heterogeneous systems deliver petaflops of peak performance to accelerate scientific discovery. In this communication, we review modern parallel accelerator architectures, mainly focusing on Intel Xeon Phi many-core devices. Xeon Phi is a relatively new platform that features tens of computing cores with hundreds of threads offering massively parallel capabilities for a broad range of application. We also discuss common parallel programming frameworks targeted to this accelerator, including OpenMP, OpenCL, MPI and HPX. Recent advances in code development for many-core devices are described to demonstrate the advantages of heterogeneous implementations over the traditional, serial computing. Finally, we highlight selected algorithms, eFindSite, a ligand binding site predictor, a force field for bio-molecular simulations, and BUDE, a structure-based virtual screening engine, to demonstrate how modern drug discovery is accelerated by heterogeneous systems equipped with parallel computing devices.

Keywords: BUDE, drug discovery, eFindSite, parallel accelerators, programming frameworks, xeon phi.

Order Reprints Order Eprints Rights & PermissionsPrintExport

Article Details

VOLUME: 17
ISSUE: 14
Year: 2016
Page: [1595 - 1609]
Pages: 15
DOI: 10.2174/1389450117666160112112854
Price: $58