3D fingerprints

Numerous examples of 3D fingerprint methods have been described in the literature, but in this review we focus only on those which can be classified as software packages or parts of them. 

Pharmacophore fingerprints represent an extension of this approach whereby a basis set of pharmacophores is generated by enumerating all pharmacophoric types with the corresponding distances between them within a specified range. The 3D fingerprint for a molecule is defined as the collection of all combina-... 

The 3D fingerprint for the receptor is compared against the 3D fingerprint for each molecule in the Catalyst database to select the top percentage of hits. There are two possible ways of comparing 3D fingerprints ... 

The first method used a similarity metric to select the top percentage of hits and the second method does the selection based only on number of common pharmacophores between the receptor active site fingerprint and the 3D fingerprint for compounds in the virtual library. Both analysis techniques are extremely fast. One of the major advantages of FLIP technology is its throughput. 

The non-binary all feature combination of the 3D fingerprint and interaction feature was able to retrieve -90% of the actives on screening 20% of the database. The Ochiai coefficient was slightly better than Tanimoto and significantly better than Dice and Hamming in retrieving actives. All features for the enzyme... 

Kulkarni, A., Karnachi, P.S., 3D fingerprint-based lead identification protocol (FLIP) application to structure based design and data mining, manuscript in preparation. 

ELAP can be used for automatic generation of site points for docking, automatic generation of 3D fingerprints descriptors for ligands and proteins ready for che-mometric analyses and lead optimization. After a brief review of the theory underpinning the ELAP software, this chapter will illustrate some of its applications and case studies. 

Rigid 3D-fingerprints consider only a single conformation of the molecule, while flexible 3D-fingerprints account for all the geometric features that can be achieved, based on a conformational exploration of the considered molecule, usually based on the incremental rotation of all the rotatable bonds. 

Table S24 Ranges of the different probes used in MOLPRINT 3D fingerprints.

Finally, the MOLPRINT 3D fingerprint is based on the set of all surface point environment descriptors. Usually descriptors obtained from different probes are treated independently. 

Flexible 3D fingerprints [74] encode interatomic distances of flexible molecules, in particular the ability to adopt a conformation with a specific atomic distance. Distances between predefined features are stored in a bitstring. 

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