What this tool does
Align-it is a tool to align molecules according to their pharmacophores. A pharmacophore is an abstract concept based on the specific interactions observed in drug-receptor interactions: hydrogen bonding, charge transfer, electrostatic and hydrophobic interactions. Molecular modeling and/or screening based on pharmacophore similarities has been proven to be an important and useful method in drug discovery.
The functionality of Align-it consists mainly of two parts. The first functionality is the generation of pharmacophores from molecules (the function of this tool). Secondly, pairs of pharmacophores can be aligned (use the tool Pharmacophore Alignment). The resulting score is calculated from the volume overlap resulting of the alignments.
Input
Example:
- database
30 31 0 0 0 0 0 0 0999 V2000
1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
- cutoff : 0.0
Output
Example:
- aligned Pharmacophores
3033
HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0
HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0
HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827
HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616
HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767
$$$$
Cite
Silicos-it - align-it