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Further study is clearly warranted using multiple diverse conformers per compound.
The present study investigates effects of employing multiple diverse conformers per compound upon 3-D similarity computation (often referred to here as "multiple-conformer effects") in two parts.
The averages for Scenario D and Scenario E were the same as those for conformer-compound pairs (Figure 3) and the unique compound-compound pairs (Figure 4), respectively, computed with multiple diverse conformers per compound.
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.
This resulted in an average throughput of 150,000 conformer pairs per second per processor core, a speed sufficient to consider multiple diverse conformers per compound in the 3-D neighboring relationship.
In the present study, 3-D similarity computations that employ a single conformer per compound and multiple diverse conformers per compound are referred to as the "single-conformer approach" and the "multiple-conformer approach", respectively.
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In the best-conformer-pair approach, a similarity score between a single conformer and a compound (or between two compounds), where each compound has multiple diverse conformations, is represented by the greatest similarity score among all conformer pairs considered per conformer-compound pair (or compound-compound pair).
Deviation of the CT-optimized 3-D similarity scores for non-inactive non-inactive (non-inactive non-inactiverom the corresponon-inactive non-inactivedom compouNN pairs, cofputed using both a single conformer and best multiple (ten) diverse conformers per compound: (a) CT-optimized ST, (b) CT-optimized CT, and (c) CT-optimized ComboT.
Deviation of the ST-optimized 3-D similarity scores for non-inactive non-inactive (non-inactive non-inactiverom the corresponon-inactive non-inactivedom compouNN pairs, cofputed using both a single conformer and best multiple (ten) diverse conformers per compound: (a) ST-optimized ST, (b) ST-optimized CT, and (c) ST-optimized ComboT.
The number of diverse conformers is much reduced by a higher diversity level.
The 3-D neighbors are different, but less so as more diverse conformers are used, illustrating the sensitivity of the input conformers to 3-D neighboring, but also how using multiple conformers during neighboring can help mitigate such effects.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com