ATCUN-derived paramagnetic distance restraints in the study of an SH3 domain
Bibliographic record
Abstract
Study of the unfolded states of proteins lends insight into the protein folding problem. A well-studied system, the unfolded state of the N-terminal drk SH3 domain, has been structurally characterized using NMR spectroscopy and other techniques. The computer program ENSEMBLE (Choy and Forman-Kay, 2001) can model the rapidly-interconverting unfolded state ensemble, based on this experimental data. To extend the constraint types usable by ENSEMBLE, the distance-dependent paramagnetic relaxation enhancement (PRE) was measured on a modified SH3 domain; a small ATCUN motif was added to the domain, which binds a paramagnetic Cu2+ ion. Models that predict the position of the copper atom fit well to the experimental PRE data, and an ENSEMBLE restraint based on PRE values was compatible with other structural information. These results support the utility of ATCUN-derived PRE data for characterization of unfolded states, an important goal in understanding protein structure, stability, and function.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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 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".