Name | Meaning | SMARTS |
---|---|---|
HA | Hydrogen Acceptor | [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]), $([#7;v3;!$([nH]);!$(*(-a)-a)])] |
HD | Hydrogen Donor | [$([O;H1,-&!$(*-N=O)]), $([S;H1&X2,-&X1]), $([#7;H;!$(*(S(=O)=O)C(F)(F)F);!$(n1nnnc1);!$(n1nncn1)]), $([#7;-])] |
Ac | Acidic Group | [$([O;H1]-[C,S,P]=O), $([*;-;!$(*~[*;+])]), $([NH](S(=O)=O)C(F)(F)F), $(n1nnnc1), $(n1nncn1)] |
Ba | Basic Group | [$([NH2]-[CX4]), $([NH](-[CX4])-[CX4]), $(N(-[CX4])(-[CX4])-[CX4]), $([*;+;!$(*~[*;-])])$(N=C-N), $(N-C=N)] |
RA | Aliphatic Ring Attachment | [$([A;D3](@*)(@*)~*)] |
AA | Aromatic Ring Attachment | [$([a;D3](@*)(@*)*)] |
HP | Hydrophobic Group | [C; !$(C-[!C]); !$(C-C-[!C]); !$(C=,#*); !$(C-C=,#*)] |
Hal | Halogen | [F,Cl,Br] |
X | Non Organic Atom | [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35] |
Using 2D descriptors has advantages and disadvantages:
Within WATER large lists of this 2D 3 Point pharmacophores are computed for each molecule. Such a list called pharmacophore key contains around 3000 features from a possible list of about 300 000.
To improve the model, keys representing multiple occurences of a feature are also used. You may recognice them by a suffix like "C=2" which means that this feature occured at least twice in this compound.
To further increase flexibility there is some fuzzyness added to the distances. The "HA 4 HA 2 Hal 4" key is also recorred as:
HA -103 HA 2 Hal 4 |
HA -104 HA 2 Hal 4 |
HA -105 HA 2 Hal 4 |
HA 4 HA -101 Hal 4 |
HA 4 HA -102 Hal 4 |
HA 4 HA -103 Hal 4 |
HA 4 HA 2 Hal -103 |
HA 4 HA 2 Hal -104 |
HA 4 HA 2 Hal -105 |
Page Owner: Alberto Gobbi - Last updated: Apr 17, 1999