Chemistry Cartridge: SIMILAR/SCORE

Daylight 4.61, dayblob 46107, Oracle Server 8.13

The Chemistry Cartridge adds the SIMILAR operator to SQL. When applied to a SMILES-containing column, rows containing structures which are similar to a given structure are selected. The binary Tanimoto coefficient is used for similarity determination: a value of 1.0 means "identical", 0.0 means "completely dissimliar". The level of similarity to be required is user-adjustable. At high levels (~0.8 or more), this is a fast, robust search type. At low levels (~0.65 or less), the results are not meaningful and result in large answer sets.

This example finds structures at least 0.80 similar to a given structure using svrmgr (rather than sqlplus to show the auxilliary operator score in action. Other examples are also available.

Oracle table: COMPOUND_118616 (nci95 structures)
Show similarity of structures at least 0.80 similar to this structure:


SVRMGR session follows (show .sql file):

Oracle Server Manager Release - Beta

(c) Copyright 1997, Oracle Corporation.  All Rights Reserved.

Oracle8 Enterprise Edition Release - Beta
With the Partitioning and Objects options
PL/SQL Release - Beta

SVRMGR> Connected.
Timing                          ON

---------- ----------- ---------------------------------------
     43894 0.873831749 O=C1CN(N=Cc2ccco2)C(=O)N1
     55940 0.876652002 [O-][N+](=O)c1ccc(C=NN2CCNC2=O)o1
     78432 0.929515421 [O-][N+](=O)c1ccc(C=NN2CC(=O)NC2=O)o1
     95811 0.800000012 OCCN1CCN(N=Cc2ccc(o2)[N+](=O)[O-])C1=O

4 rows selected.
Parse             0.00 (Elapsed)     0.00 (CPU)
Execute/Fetch     0.92 (Elapsed)     0.00 (CPU)
Total             0.92               0.00
Timing                          OFF
Server Manager complete.

Daylight Chemical Information Systems, Inc.