Using Shape Descriptors to Filter Molecular Shapes in PubChem
Author Information
Author(s): Kim Sunghwan, Bolton Evan E, Bryant Stephen H
Primary Institution: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
Hypothesis
Can additional shape descriptor relationships improve the filtering efficacy of molecular shape comparisons in PubChem?
Conclusion
Basic shape descriptors can effectively identify incompatible compound conformer pairs, improving computational efficiency in 3-D shape searches.
Supporting Evidence
- The study analyzed 4.18 billion 3-D neighbor pairs to assess shape compatibility.
- Filters based on shape descriptors improved throughput by 31% in PubChem 3-D neighboring.
- The monopole-based quadrupole filters showed the best performance in filtering out non-neighbor pairs.
Takeaway
This study shows that we can use simple measurements of shape, like length and width, to quickly find molecules that don't fit together, making searches faster.
Methodology
The study analyzed 4.18 billion 3-D neighbor pairs from 17.1 million molecules, using shape descriptors to filter out incompatible pairs.
Limitations
The filters may exclude some potential neighbors, but the loss is negligible compared to the efficiency gained.
Statistical Information
P-Value
p<0.05
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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