A Quantitative Approach to the Estimation of Chemical Space from a Given Geometry by the Combination of Atomic Species
Why this work is in the frame
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Bibliographic record
Abstract
Abstract In order to estimate the size of chemical spaces, a quantitative approach was employed consisting of summing all possible combinations of atomic species generated computationally for a given three‐dimensional geometry. The atomic species were comprised of heavy atoms (N, C, O, S and Cl) and various numbers of H atoms ( e.g. , CH 3 and CH 2 groups). The assignment of atomic species to a given geometry maintained consistent bond orders between adjacent atoms. Between 10 8 and 10 19 compounds were generated from individual geometries. A slightly smaller number of compounds were obtained by applying a nonleadlikeness filter that considered the properties of the substituents. Principal component analysis using descriptors representing the molecular structures and properties revealed that the compounds generated from only one geometry largely covered the chemical space of known compounds. Moreover, the compounds with the best scores, defined as the interaction energies between the compounds and the protein, contained original ones within the entire collection of compounds generated from the same geometry. This method can be used to improve the scaffold of compound structures during drug development.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.004 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.003 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it