PharmCast · Fingerprint

Fingerprint a molecule

Draw one structure. PharmCast predicts its complete 3D pharmacophore fingerprint from the 2D structure alone and shows you the whole thing: which of the 10,549 pharmacophores are set, what each one is as a feature triplet, and the fingerprint itself, ready to copy. No conformers are generated at any point.

Compare two molecules Pharmacophore fingerprints, explained PharmCast home
A three-point pharmacophore: three typed features p1, p2 and p3 joined by three measured distances, beside the seven feature types and six distance bins that enumerate 10,549 pharmacophores.
What one pharmacophore is. Three typed features and the three binned distances between them. Seven feature types and six distance bins, enumerated over every triangle that satisfies the triangle inequality on the bin bounds, give 10,549 distinct pharmacophores. Every one that this molecule can present in some accessible conformation is listed below by name.

1 · The molecule

You do not have to draw it. To use a SMILES string, press the editor's Open Structure button, the folder icon at the top left, and choose Paste from clipboard: it accepts SMILES and will draw the molecule for you.

2 · Run PharmCast

Nothing drawn yet? Load montelukast, a 586 Da drug that reaches every distance bin including the longest.

Every position in a pharmacophore fingerprint is a named, geometric thing: three typed features at three binned distances. That is why the hit list above reads as chemistry rather than as an opaque bit index, and why two molecules from unrelated scaffolds can set the same position. These are ensemble fingerprints, so a set pharmacophore means this molecule can present that triangle in some accessible conformation, not that it always does.

Method, measurements and the training corpora: pharmacophore fingerprints, explained. To compare two molecules rather than fingerprint one, use the compare page.