Neighbor_Search: General Usage & Hints

Neighbor_Search calculates the "neighborhood" for compound(s) which are input by the user.

Compounds may be input in two formats:

Once the compound is input, one or more databases to search against may be selected. The default is to search only the SC database.

Finally, a similarity range may be input. This range represents similarity as measured by the Tanimoto Coefficient (Tc) between molecules characterized by the Daylight fingerprint. The Tc ranges from 1.0 (highest homology) to 0,0 (no homology). Extensive experience with this similarity measure suggests that a range from 1.0 to 0.70 (the default values in Neighbor_Search) seems optimal for a first pass. If too many compounds are found using these values, the lower bound should be raised from 0.70. Likewise, if too few compounds are found, the range may be expanded by decreasing the lower bound. Research at Abbott Laboratories with the Tc/Daylight fingerprint suggests that, on average, relatively high homology (Tc >= 0.85) is required in order to see similarity in terms of biological activity.