MoonProt 3.0: an update of the moonlighting proteins database
Bibliographic record
Abstract
MoonProt 3.0 (http://moonlightingproteins.org) is an updated open-access database storing expert-curated annotations for moonlighting proteins. Moonlighting proteins have two or more physiologically relevant distinct biochemical or biophysical functions performed by a single polypeptide chain. Here, we describe an expansion in the database since our previous report in the Database Issue of Nucleic Acids Research in 2018. For this release, the number of proteins annotated has been expanded to over 500 proteins and dozens of protein annotations have been updated with additional information, including more structures in the Protein Data Bank, compared with version 2.0. The new entries include more examples from humans, plants and archaea, more proteins involved in disease and proteins with different combinations of functions. More kinds of information about the proteins and the species in which they have multiple functions has been added, including CATH and SCOP classification of structure, known and predicted disorder, predicted transmembrane helices, type of organism, relationship of the protein to disease, and relationship of organism to cause of disease.
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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 | 0.003 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.007 | 0.006 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.004 | 0.003 |
| Open science | 0.003 | 0.003 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.020 | 0.028 |
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".