An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization

Journal of Chemical Information and Computer Sciences

Volumn 40, Issue 1, 2000, Pages 167-177

  Dexuan, Xie ^a,d   Tropsha, Alexander ^b,c   Schlick, Tamar ^a  

^a NEW YORK UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d The University of Southern Mississippi   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL STRUCTURE; DATA BASE; THEORETICAL MODEL;

DATABASE MANAGEMENT SYSTEMS; MODELS, THEORETICAL; MOLECULAR STRUCTURE;

EID: 0033630049     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci990333j     Document Type: Article

References (23)

1. Molconn-Z, version 3.1; Hall Associates Consulting: Quincy, MD, 1998.
2. Molconn-X, version 2.0; Hall Associates Consulting: Quincy, MD, 1995.
3. NAG Fortran Library, Mark 17; NAG Inc.: Opus Place, Suite 200, Downers Grove, IL, 1995.
4. Agrafiotis, D. K. A new method for analyzing protein sequence relationships based on Sammon maps. Protein Sci. 1997, 6, 287-293.
5. Boyd, D. B. Rational drug design: Controlling the size of the haystack. Mod. Drug. Discov. 1998, 1, 41-47.
6. Bakonyi, M.; Johnson, C. R. The Euclidean distance matrix completion problem. SIAM J. Matrix Anal. Appl. 1995, 16, 646-654.
7. Brown, R. D.; Martin, Y. C. Information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. J. Chem. Inf. Comput. Sciences, 1997, 37, 1-9.
8. Crippen, G. M.; Havel, T. F. Distance Geometry and Molecular Conformation; Wiley, New York, 1988.
9. Glunt, W.; Hayden, T. L.; Hong, S.; Wells, J. An alternating projection algorithm for computing the nearest Euclidean distance matrix. SIAM J. Matrix Anal. Appl. 1990, 11, 589-600.
10. Golub, G. H.; Van Loan, C. F. Matrix Computations, 3rd ed.; John Hopkins University Press: Baltimore, MD, 1996.
11. Gower, J. C. Properties of Euclidean and non-Euclidean distance matrices. Linear Algebra Appl. 1985, 67, 81-97.
12. Hassan, M.; Bielawski, J. P.; Hempel, J. C.; Waldman, M. Optimization and visualization of molecular diversity and combinatorial libraries. Mol. Divers. 1996, 2, 64-74.
13. Kohonen, T. Self-Organizing Maps, Springer Series in Information Sciences; Springer: Berlin, Heidelberg, New York, 1997; Vol. 30.
14. MACCS-II; Molecular Design Ltd.: 14600 Catalina St., San Leandro, CA 94577, 1998.
15. Moré, J. J.; Wu, Z. Distance geometry optimization for protein structures; MCS-P628-1296; Argonne National Laboratory: Argonne, IL, 1997.
16. Pinou, T., Schlick, T., Li, B.; Dowling, H. G. Addition of Darwin's third dimension to phyletic trees. J. Theor. Biol. 1996, 182, 505-512.
17. Robinson, D. D.; Barlow, T. W.; Richard, W. G. Reduced dimensional representations of molecular structure. J. Chem. Inf. Comput. Sci. 1997, 37, 939-942.
18. Schlick, T.; Fogelson, A. TNPACK-A truncated Newton minimization package for large-scale problems: I. Algorithm and usage. ACM Trans. Math. Softw. 1992, 14, 46-70.
19. Shemetulskis, N.; Dunbar, J., Jr.; Dunbar, B.; Moreland, D.; Humblet, C. Enhancing the diversity of a corporate database using chemical database clustering and analysis. Comput.-Aided Mol. Des. 1995, 9, 407-416.
20. Xie, D.; Schlick, T. Efficient implementation of the truncated-Newton algorithm for large-scale chemistry applications. SIAM J. Optim. 1999, in press.
21. Xie, D.; Schlick, T. Remark on Algorithm 702-the updated truncated Newton minimization package. ACM Trans. Math. Softw. 1999, 25, 108-122.
22. Xie, D.; Schlick, T. Visualization of chemical databases using the singular value decomposition and truncated-Newton minimization. Preprint, submitted to Optimization in Computational Chemistry and Molecular Biology; Floudas, A., Pardalos, P. M., Eds.; Kluwer Academic Publishers B. V.: Dordrecht, The Netherlands, in press.
23. Willett, P. Structural similarity measures for database searching. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Editor-in-Chief; Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer, H. F., III, Eds.; John Wiley & Sons: West Sussex, U.K. 1998; Vol. 4, pp 2748-2756.