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
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.008 | 0.001 |
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".