Analyzing the 3D Structure of Human Carbonic Anhydrase II and Its Mutants Using Deep View and the Protein Data Bank
Why this work is in the frame
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Bibliographic record
Abstract
A lab was designed to teach biological chemistry students to critically analyze the 3D structure of a protein. The enzyme studied was human carbonic anhydrase (II) and students also examined mutants and protein bound to a variety of ligands, metals, and inhibitors. The coordinate files for each protein are downloaded by the students from the Protein Data Bank. The structure is viewed and manipulated with the public-domain molecular-viewing software Deep View. Students learn how to interpret Ramachandran plots, study familial homology, make virtual mutations, compare structures, analyze structural details, and produce stunning 3D images. The lab runs on personal computers with Internet access and requires minimal to no supervision. This lab can be used as an independent project or as part of a more comprehensive set of experiments, and it can be adapted to the study of other biomolecules.
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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 | 0.000 | 0.000 |
| 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 | 0.000 | 0.000 |
| 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