Ultrafast shape recognition for similarity search in molecular databases

Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences

Volumn 463, Issue 2081, 2007, Pages 1307-1321

  Ballester, Pedro J ^a   Richards, W Graham ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Data explosion; Molecular shape comparison; Pattern recognition; Similarity search; Virtual screening

Indexed keywords

EID: 36349009372     PISSN: 13645021     EISSN: 14712946     Source Type: Journal    
DOI: 10.1098/rspa.2007.1823     Document Type: Article

References (24)

1. Albrecht, B., Grant, G. H. & Richards, W. G. 2004 Evaluation of structural similarity based on reduced dimensionality representations of protein structure. Protein Eng. Design Select. 17, 425-432. (doi:10.1093/protein/gzh049)
2. Baringhaus, K.-H. & Hessler, G. 2004 Fast similarity searching and screening hit analysis. Drug Discov. Today: Technol. 1, 197-202. (doi:10.1016/j.ddtec.2004.11.001)
3. Bemis, G. W. & Kuntz, I. D. 1992 A fast and efficient method for 2D and 3D molecular shape description. J. Comput. Aid. Mol. Des. 6, 607-628. (doi:10.1007/BF00126218)
4. Bender, A. & Glen, R. C. 2004 Molecular similarity: a key technique in molecular informatics. Org. Biomol. Chem. 2, 3204-3218. (doi:10.1039/b409813g)
5. Böhm, H.-J., Flohr, A. & Stahl, M. 2004 Scaffold hopping. Drug Discov. Today: Technol. 1, 217-224. (doi:10.1016/j.ddtec. 2004.10.009)
6. Claus, B. L. & Underwood, D. J. 2002 Discovery informatics: its evolving role in drug discovery. Drug Discov. Today 7, 957-966. (doi:10.1016/S1359-6446(02)02433-9)
7. Funkhouser, T., Kazhdan, M., Min, P. & Shilane, P. 2005 Shape-based retrieval and analysis of 3D models. Commun. ACM 48, 58-64. (doi:10.1145/1064830.1064859)
8. Good, A. C. & Richards, W. G. 1998 Explicit calculation of 3D molecular similarity. Perspect. Drug Discov. Des. 9-11, 321-338. (doi:10.1023/A:1027280526177)
9. Good, A. C., Ewing, T. J. A., Gschwend, D. A. & Kuntz, I. D. 1995 New molecular shape descriptors: application in database screening. J. Comput. Aid. Mol. Des. 9, 1-12. (doi:10.1007/BF00117274)
10. Hahn, M. 1997 Three-dimensional shape-based searching of conformationally flexible compounds. J. Chem. Inf. Comput. Sci. 37, 80-86. (doi:10.1021/ci960108r)
11. Jenkins, J. L., Glick, M. & Davies, J. W. 2004 A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes. J. Med. Chem. 47, 6144-6159. (doi:10.1021/jm049654z)
12. Kola, I. & Hazuda, D. 2005 Innovation and greater probability of success in drug discovery and development - from target to biomarkers. Curr. Opin. Biotechnol. 16, 644-646. (doi:10.1016/j.copbio.2005.10.014)
13. Kotani, T. & Higashiura, K. 2002 Rapid evaluation of molecular shape similarity index using pairwise calculation of the nearest atomic distances. J. Chem. Inf. Comput. Sci. 42, 58-63. (doi:10.1021/ci010068d)
14. Mason, J. S., Morize, I., Menard, P. R., Cheney, D. L., Hulme, C. & Labaudiniere, R. F. 1999 New 4-point pharmacophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J. Med. Chem. 42, 3251-3264. (doi:10.1021/jm9806998)
15. MOE, 2006.08 release. (http://www.chemcomp.com/)
16. Muggleton, S. H. 2006 Exceeding human limits. Nature 440, 409-410. (doi:10.1038/440409a)
17. Nilakantan, R., Bauman, N. & Venkataraghavan, R. 1993 New method for rapid characterisation of molecular shapes: applications in drug design. J. Chem. Inf. Comput. Sci. 33, 79-85. (doi:10.1021/ci00011a012)
18. Richards, W. G. 2002 Virtual screening using GRID computing: the screensaver project. Nat. Rev. Drug Discov. 1, 551-555. (doi:10.1038/nrd841)
19. Rush III, T. S., Grant, J. A., Mosyak, L. & Nicholls, A. 2005 A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J. Med. Chem. 48, 1489-1495. (doi:10.1021/jm040163o)
20. Schnecke, V. & Boström, J. 2006 Computational chemistry-driven decision making in lead generation. Drug Discov. Today 11, 43-50. (doi:10.1016/S1359-6446(05)03703-7)
21. Szalay, A. & Gray, J. 2006 Science in an exponential world. Nature 440, 413-414. (doi:10.1038/440413a)
22. Willett, P. 2005a Searching techniques for databases of two- and three-dimensional chemical structures. J. Med. Chem. 48, 4183-4199. (doi:10.1021/jm0582165)
23. Willett, P. 2005b Chemoinformatics techniques for data mining in files of two-dimensional and three-dimensional chemical molecules. In Proc. FIS2005, F69, pp. 1-15. (http://www.mdpi.org/fis2005/proceedings.html)
24. Zauhar, R. J., Moyna, G., Tian, L., Li, Z. & Welsh, W. J. 2003 Shape signatures, a new approach to computer-aided ligand- and receptor-based drug design. J. Med. Chem. 46, 5674-5690. (doi:10.1021/jm030242k)