FakeRotLib: Expedient Noncanonical Amino Acid Parametrization in Rosetta
Bibliographic record
Abstract
Noncanonical amino acids (NCAAs) occupy an important place, both in natural biology and in synthetic applications. However, modeling these amino acids still lies outside the capabilities of most deep learning methods due to sparse training data sets for this task. Instead, biophysical methods such as Rosetta can excel in modeling NCAAs. We discuss the various aspects of parametrizing an NCAA for use in Rosetta, identifying rotamer distribution modeling as one of the most impactful factors of NCAA parametrization on Rosetta performance. To this end, we also present FakeRotLib, a method that uses statistical fitting of small-molecule conformers to create rotamer distributions. We find that FakeRotLib outperforms existing methods in a fraction of the time and is able to parametrize NCAA types previously unmodeled by Rosetta.
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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 | 0.004 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.004 |
| Insufficient payload (model declined to judge) | 0.012 | 0.006 |
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".