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

COMPOUND_I SCORE(1)    SMILES                                                                          
---------- ---------- --------------------------------------------------------------------------------
      5406 0.847058833 CC(=CC=O)C=CC=C(C)C=CC1=C(C)CCCC1(C)C
     44930 0.855263174 C1CCC(=CC1)C2=CCCCC2
     46634 1.000000000 CC(=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)CCCC1(C)C)C=CC=C(C)C=CC2=C(C)CCCC2(C)C
     53509 0.825581372 CC(=CC=O)C=CC1=C(C)CCCC1(C)C
     94006 0.837209284 CC(=CCO)C=CC=C(C)C=CC1=C(C)CCCC1(C)C

5 rows selected.
Parse             0.00 (Elapsed)     0.00 (CPU)
Execute/Fetch     0.97 (Elapsed)     0.00 (CPU)
Total             0.97               0.00
Timing                          OFF
Server Manager complete.

Daylight Chemical Information Systems, Inc.