Small Molecules as Rotamers: Generation and Docking in RosettaLigand.
Bibliographic record
Abstract
Abstract: We introduce small molecule rotamers into the rotamer search protocol used in Rosetta to model small molecule flexibility in docking. Rosetta, a premier protein modeling suite, models side chain flexibility using discrete conformations observed in the Protein Data Bank (PDB). We mimic this concept and build small molecule rotamers based on conformations from the Cambridge Structural Database. We eval-uate to the small molecule rotamer generation protocol on a test set of 628 conforma-tion,s taken from the PDBBind database, of small molecules with ≤ 6 rotable bonds. Our protocol generates ensembles in which the closest conformation is 0.45 ±0.31 A RMSD from the crystallized conformation. Further, in a set of 21 small molecule pro-tein complexes, 16 of 21 cases a native-like model was in the top 1 % of models by energy. 1
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.011 | 0.004 |
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 itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".