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Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics

[ Vol. 22 , Issue. 23 ]

Author(s):

Yoshifumi Fukunishi, Tadaaki Mashimo, Kiyotaka Misoo, Yoshinori Wakabayashi, Toshiaki Miyaki, Seiji Ohta, Mayu Nakamura and Kazuyoshi Ikeda   Pages 3555 - 3568 ( 14 )

Abstract:


Background: Computer-aided drug design is still a state-of-the-art process in medicinal chemistry, and the main topics in this field have been extensively studied and well reviewed. These topics include compound databases, ligand-binding pocket prediction, protein-compound docking, virtual screening, target/off-target prediction, physical property prediction, molecular simulation and pharmacokinetics/pharmacodynamics (PK/PD) prediction. Message and Conclusion: However, there are also a number of secondary or miscellaneous topics that have been less well covered. For example, methods for synthesizing and predicting the synthetic accessibility (SA) of designed compounds are important in practical drug development, and hardware/software resources for performing the computations in computer-aided drug design are crucial. Cloud computing and general purpose graphics processing unit (GPGPU) computing have been used in virtual screening and molecular dynamics simulations. Not surprisingly, there is a growing demand for computer systems which combine these resources. In the present review, we summarize and discuss these various topics of drug design.

Keywords:

Computer-aided drug design, Synthetic accessibility, Cloud computing, GPU computing, Virtual screening, Molecular dynamics simulation.

Affiliation:

Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan



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