Molecular Dynamics Study of the Beta Amyloid Peptide of Alzheimer's Disease and Its Divalent Copper Complexes
Bibliographic record
Abstract
The Abeta1-42 monomer structure was assessed with a 790 ns molecular dynamics (MD) simulation, and the results were compared with the NMR experiment on Abeta10-35 and Abeta1-40. Previous theoretical work in a model of the His13-His14 region of Abeta defined the possible Cu(II) binding geometries at this site (Raffa et al. J. Biol. Inorg. Chem. 2005, 10, 887-902). MD simulations totalling almost 2 micros were also carried out on Cu(II)/Abeta1-42 systems, using the ab initio structures as templates for the copper binding site. This work finds that the copper-free Abeta1-42 system may stabilize after approximately 350 ns into a collapsed coil conformation, and we find good agreement with some, but not all, of the structural features determined experimentally for the Abeta10-35 and Abeta1-40 peptides. The results of the Cu(II)/Abeta1-42 systems are compared to the Cu(II)-free Abeta1-42 simulation.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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 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".