ULaval: K. pneumoniae TBDT with plug model
Bibliographic record
Abstract
To better understand the importance of the plug domain as a structural component of the TBDT, we employed molecular dynamics simulations, which enable us to analyze how the different parts of the protein interact and behave over time. To do so, we first had to acquire a structure of Klebsiella Pneumonia’s TBDT. Since none were found at the beginning of this iGEM cycle, and considering that a high degree of structural conservation is observed between all TBDTs, we opted to predict the structure using Alphafold3 and Chai-1 .To do so, we use the sequence from the Uniprot entry Q6U607 as an input sequence for both predictions. Both models predicted similar structures, with the two of them presenting a root mean square deviation (rmsd) of only 0.958 Å. In this case, the rmsd reflects the average distance between two atoms of superimposed structures. A lower rmsd therefore, reflects a high similarity between the structures. To create the biomodelling system, we used the structure generated from AlphaFold3. https://2025.igem.wiki/ulaval/home
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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) | 0.004 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.001 |
| Open science | 0.005 | 0.002 |
| Research integrity | 0.005 | 0.003 |
| Insufficient payload (model declined to judge) | 0.022 | 0.037 |
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".