Molecular Docking and Dynamics of CePNKP Phosphatase Binding to the ss-5-Mer TCCTC
Bibliographic record
Abstract
Polynucleotide kinase/phosphatase (PNKP) is a DNA repair enzyme found in mammals, which recognizes and repairs DNA backbone breaks with 3'-phosphate and 5'-hydroxyl ends. DNA can be damaged by ionizing radiation, chemical agents and enzymatic action. The phosphatase domain of PNKP recognizes the 3'-phosphate group, excises it, and replaces it with a 3'-hydroxyl group, thereby making the 3'-end ready for the action of a ligase that completes the DNA strand. In this work, the single-stranded 5-mer TCCTC sequence was docked to the phosphatase domain of the C. elegans PNKP using the Modeller interface implemented in the UCSF Chimera software, taking into account the crystallographic information available. The structure of the complex was subject to a classical molecular dynamics protocol using Gromacs. Molecular dynamics is a computer simulation technique that allows us to compute dynamic and thermodynamic properties to determine the physical interaction between the PNKP phosphatase and the ssDNA. Department: Physical Sciences Faculty Mentor: Dr. Jorge Llano
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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 | 0.001 | 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 | 0.001 |
| 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".