Constructing a foundational platform driven by Japan's K supercomputer for next-generation drug design

Molecular Informatics

Volumn 33, Issue 11-12, 2014, Pages 732-741

  Brown, J B ^a,b   Nakatsui, Masahiko ^c,d   Okuno, Yasushi ^a,b,d  

^a KYOTO UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b FOUNDATION FOR BIOMEDICAL RESEARCH AND INNOVATION   (Japan)

^c KOBE UNIVERSITY   (Japan)

^d RIKEN   (Japan)

Author keywords

Chemogenomics; Drug design; Free energy calculation; Molecular dynamics; Virtual screening

Indexed keywords

BIG DATA; BINDING ENERGY; COSTS; DATA HANDLING; DIAGNOSIS; FREE ENERGY; SUPERCOMPUTERS;

BINDING FREE ENERGY; CHEMOGENOMICS; DATA PROCESSING METHODS; DRUG DESIGN; DRUG DISCOVERY; FREE-ENERGY CALCULATIONS; MEDICAL SYSTEMS; REDUCE COSTS; STRUCTURAL SIMULATIONS; VIRTUAL SCREENING;

MOLECULAR DYNAMICS;

ACCURACY; ALGORITHM; COMPARATIVE STUDY; COMPUTER; COMPUTER SIMULATION; DRUG DESIGN; DRUG INDUSTRY; ENERGY; HIGH THROUGHPUT SCREENING; JAPAN; LARGE SCALE PRODUCTION; MOLECULAR DYNAMICS; PHARMACEUTICAL ENGINEERING; PREDICTION; PROTEIN INTERACTION; REVIEW; SUPERCOMPUTER;

EID: 84915788123     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201400067     Document Type: Review

References (10)

1. A. Yonezawa, T. Watanabe, M. Yokokawa, M. Sato, K. Hirao, "Advanced Institute for Computational Science (AICS): Japanese National High-Performance Computing Research Institute and Its 10-petaflops Supercomputer "K" ", in Proc. 2011 Int. Conf. for High Performance Computing, Networking, Storage and Analysis (SC'11), 1-8 2011.
2. R. Bohacek, C. McMartin, W. Guida, Med. Res. Rev. 1996, 16, 3-50.
3. H. Yabuuchi, S. Niijima, H. Takematsu, T. Ida, T. Hirokawa, T. Hara, T. Ogawa, Y. Minowa, G. Tsujimoto, Y. Okuno, Mol. Syst. Biol. 2011, 7, 472.
4. J. B. Brown, S. Niijima, Y. Okuno, Mol. Inf. 2013, 32, 906-921.
5. H. Fujitani, Y. Tanida, A. Matsuura, Phys. Rev. E 2009, 021914.
6. C. Cortes and V. Vapnik, Machine Learning 1995, 20, 273-297.
7. E. Bolton, Y. Wang, P. Thiessen, S. Bryant, "PubChem: Integrated Platform of Small Molecules and Biological Activities", in Annu. Rep. Comput. Chem. , Volume 4, 2008.
8. A. Gaulton, L. J. Bellis, A. P. Bento, J. Chambers, M. Davies, A. Hersey, Y. Light, S. McGlinchey, D. Michalovich, B. Al-Lazikani, J. P. Overington, Nucleic Acids Res. 2012, 40 (D1), D1100-D1107.
9. C. Jarzynski, Phys. Rev. Lett. 1997, 78, 2690.
10. J. Dunbar Jr., R. D. Smith, C.-Y. Yang, P. M.-U. Ung, K. W. Lexa, N. A. Khazanov, J. A. Stuckey, S. Wang, H. A. Carlson, J. Chem. Inf. Model. 2011, 51, 2036-2046.