Advanced in-silico drug screening to achieve high hit ratio

Synthesiology

Volumn 2, Issue 1, 2009, Pages 64-72

  Fukunishi, Yoshifumi ^a   Sugihara, Yuusuke ^b   Mikami, Yoshiaki ^c   Sakai, Kohta ^b   Kusudo, Hiroshi ^c   Nakamura, Haruki ^d  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b FUJITSU LABORATORIES LTD   (Japan)

^c Hitachi Solutions   (Japan)

^d OSAKA UNIVERSITY   (Japan)

Author keywords

Compound database; Compound library; In silico drug screening; MyPresto; Virtual screening

Indexed keywords

EID: 77749298913     PISSN: 18830978     EISSN: None     Source Type: Journal    
DOI: 10.5571/syntheng.2.64     Document Type: Article

References (20)

1. http://www.mdl.com/jp/products/experiment/cims/index.jsp
2. http://www.molecular-networks.com/software/corina/index.html
3. M. Hattori, Y. Okuno, S. Gotoand M. Kanahisa: Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc., 125 (39), 11853-11865 (2003).
4. J. Gasteiger and T. Engel: Chemoinformatics: A textbook. WILEY-VCH: Weinheim. (2003).
5. http://www.lmcp.jussieu.fr/sincris-top/logiciel/prg-babel.html
6. http://openbabel.org/wiki/Main-Page
7. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case: Development and testing of a general amber force field. J. Compt. Chem., 25 (9), 1157-1174 (2004).
8. http://www.ccdc.cam.ac.uk/products/csd/
9. Y. Fukunishi, Y. Mikami and H. Nakamura: The filling potential method: A method for estimating the free energy surface for protein-ligand docking. J. Phys. Chem. B. 107 (47), 13201-13210 (2003).
10. J. Gasteiger and M. Marsili: A new model for calculating atomic charges in molecules. Tetrahedron Lett., 3181-3184 (1978).
11. http://openmopac.net/index.html
12. J. Wang, P. Cieplak and P.A. Kollman: How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21 (12), 1049-1074 (2000).
13. Y. Fukunishi, Y. Mikami and H. Nakamura: Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening. J. Mol. Graph. and Model., 24 (1), 34-45 (2005).
14. Y. Fukunishi, Y. Mikami, K. Takedomi, M. Yamanouchi, H. Shima and H. Nakamura: Classification of chemical compounds by protein-compound docking for use in designing a focused library. J. Med. Chem., 49 (2), 523-533 (2006).
15. Y. Fukunishi, Y. Mikami, S. Kubota and H. Nakamura: Multiple target screening method for robust and accurate in silico ligand screening. J. Mol. Graph. and Model. 25 (1), 61-70 (2005).
16. Y. Fukunishi, S. Kubota and H. Nakamura: Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening. J. Chem. Info. Mod., 46 (5), 2071-2084 (2006).
17. Y. Fukunishi, S. Hojo and H. Nakamura: An efficient in silico screening method based on the protein-compound affinity matrix and its application to the design of a focused library for cytochrome P450 (CYP) ligands. J. Chem. Info. Mod., 46 (6), 2610-2622 (2006).
18. http://presto.protein.osaka-u.ac.jp/myPresto4/index-e.html
19. http://presto.protein.osaka-u.ac.jp/LigandBox/web-search.cgi
20. J. J. Irwin and B. K. Shoichet: ZINC-a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model., 45 (1), 177-182 (2005).