Table 1.
Different 3-D similarity search (or analysis) scenarios considered
| Search Scenario | Query | Conformer model | Description |
|---|---|---|---|
| A |
Compound |
Single conformer |
Similarity scores for a compound “query” compared to those of the “database” compounds, both computed using a single conformer per compound. |
| B |
Compound |
Multiple conformer, All-conformer-pair approach |
Similarity scores that one may expect when each “query” conformer is compared to a set of multiple diverse conformers of the “database” compounds, using the “all-conformer-pair” approach. That is, all unique conformer pairs contribute to the average and standard deviation of the resulting similarity scores. |
| C |
Conformer |
Multiple conformer, All-conformer-pair approach |
Similarity scores that one may expect when a single “query” conformer is compared to a set of multiple diverse conformers of the “database” compounds, using the “all-conformer-pair” approach. That is, all unique conformer pairs contribute to the average and standard deviation of the resulting similarity scores. |
| D |
Conformer |
Multiple conformer, Best-conformer-pair approach |
Similarity scores that one may expect when a single “query” conformer is compared to a set of multiple diverse conformers of the “database” compounds using the “best-conformer-pair” approach. That is, only the conformer pair with the greatest similarity per conformer-compound pair contributes to the average and standard deviation of the resulting similarity scores. |
| E | Compound | Multiple conformer, Best-conformer-pair approach | Similarity scores that one may expect when each “query” conformer is compared to a set of multiple diverse conformers of the “database” compounds using the “best-conformer-pair” approach. That is, only the conformer pair with the greatest similarity per compound-compound pair contributes to the average and standard deviation of the resulting similarity scores. |
Five different conformer handling scenarios considered in this study, where the 3-D similarity “query” is the entity being compared to a “database” of compound conformers.