After 3DMET Release 2.0, substructure search is available. This supplys a simple
database search by using SMILES. However, three level of the search can be applied
by the difference about database description and search keys made by the editor. The
difference among three levels are shown as below.
- Level 3: Ignore atom chiralities
- Level 2: [level 3 set] + Ignore charge + Ignore subset definition
- Level 1: [level 2 set] + Ignore bond types
For the ignoring characters in the SMILES string, the search becomes stricter on
the order from the level 3 to level 1. Two results comparing three levels are
shown in the Table 1.
Table 1. Examples for the three levels of the substructure search
|
Query = benzene |
Query = phenol |
| Level |
hit number |
an example |
hit number |
an example |
| Level 3 |
565 |
|
30 |
|
| Level 2 |
730 |
4-aminobenzoate (B00134) |
317 |
formonectin (B00192) |
| Leve 1 |
815 |
cyclohexylamine (B00135) |
351 |
cyclohesanone (B00106) |
|
Query = 1,3-butadiene |
Query = n-octane |
| Level |
hit number |
an example |
hit number |
an example |
| Level 3 |
142 |
|
193 |
|
| Level 2 |
221 |
retinal (B00095) |
222 |
Undecaprenyl phosphate (B00093) |
| Leve 1 |
3322 |
L-lysine (B00013) |
433 |
Arachidonic acid (B00061) |
It must be paied attention that this result has possible false negatives,
because all substructure will not be described as the one sub-string in the whole
SMILES string, even if by using canonical SMILES.
|
Substructure search 