Latent semantic structure indexing (LaSSI) for defining chemical similarity

被引:30
作者
Hull, RD [1 ]
Singh, SB [1 ]
Nachbar, RB [1 ]
Sheridan, RP [1 ]
Kearsley, SK [1 ]
Fluder, EM [1 ]
机构
[1] Merck Res Labs, Dept Mol Syst, Rahway, NJ 07065 USA
关键词
D O I
10.1021/jm000393c
中图分类号
R914 [药物化学];
学科分类号
100701 ;
摘要
A novel method for computing chemical similarity from chemical substructure descriptors is described. This new method, called LaSSI, uses the singular value decomposition (SVD) of a chemical descriptor-molecule matrix to create a low-dimensional representation of the original descriptor space. Ranking molecules by similarity to a probe molecule in the reduced-dimensional space has several advantages over analogous ranking in the original descriptor space: matching latent structures is more robust than matching discrete descriptors, choosing the number of singular values provides a rational way to vary the "fuzziness" of the search, and the reduction in the dimensionality of the chemical space increases-searching speed. LaSSI also allows the calculation of the similarity between two descriptors and between a descriptor and a molecule.
引用
收藏
页码:1177 / 1184
页数:8
相关论文
共 29 条
[1]   SIMILARITY SEARCHING IN FILES OF 3-DIMENSIONAL CHEMICAL STRUCTURES - COMPARISON OF FRAGMENT-BASED MEASURES OF SHAPE SIMILARITY [J].
BATH, PA ;
POIRRETTE, AR ;
WILLETT, P ;
ALLEN, FH .
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 1994, 34 (01) :141-147
[2]  
BERRY M, 1996, SVDPAKC VERSION 1 0
[3]   The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding [J].
Brown, RD ;
Martin, YC .
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 1997, 37 (01) :1-9
[4]   Use of structure Activity data to compare structure-based clustering methods and descriptors for use in compound selection [J].
Brown, RD ;
Martin, YC .
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 1996, 36 (03) :572-584
[5]   ATOM PAIRS AS MOLECULAR-FEATURES IN STRUCTURE ACTIVITY STUDIES - DEFINITION AND APPLICATIONS [J].
CARHART, RE ;
SMITH, DH ;
VENKATARAGHAVAN, R .
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 1985, 25 (02) :64-73
[6]  
DEERWESTER S, 1990, J AM SOC INFORM SCI, V41, P391, DOI 10.1002/(SICI)1097-4571(199009)41:6<391::AID-ASI1>3.0.CO
[7]  
2-9
[8]  
DOWNS GM, 1995, REV COMP CH, V7, P1
[9]  
DUMAIS S, 1994, TREC 3 P GAITH MD, P219
[10]  
Dunn III W. J., 1989, TETRAHEDRON COMPUT M, V2, P349, DOI DOI 10.1016/0898-5529(89)90004-3