Analysis of Fbox substrate adapter proteins using <i>ProteoSync</i> , a program for projection of evolutionary conservation onto protein atomic coordinates
Bibliographic record
Abstract
<h2>Abstract</h2> The projection of conservation onto the surface of a protein's 3D structure is a powerful way of inferring functionally important regions. For this reason, we created ProteoSync, a Python program that semi-automates the process. The program creates an annotated sequence alignment of orthologs from a diverse set of selectable species and enables the fast projection of amino acid conservation onto a predicted or known 3D model in PyMOL <sup>1</sup>. As a test case, we used ProteoSync to analyze a subset of 31 F-box proteins, which function as substrate recognition subunits for a large family of Cul1-based E3 ubiquitin ligases. We correctly identified known substrate interaction surfaces for 11 F-box members with previously solved structures. We also identified likely ligand binding sites for 16 other members, thus demonstrating ProteoSync's utility for discovering conserved, functionally relevant surfaces.
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How this classification was reachedexpand
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 itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, 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".