Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch using Well-Tempered Metadynamics Simulations input and output files
Bibliographic record
Abstract
The MD simulation data for the research article: - Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch using Well-Tempered Metadynamics Simulations Standard_md_files.zip: The Standard_md folder comprises the initial conformations and prepared system files for both apo proteins and ligand-protein complexes. It also includes all topology files and coordinate files (.prmtop & .rst7) required for each system. Amber_md_input.zip: The Amber_input folder encompasses a comprehensive set of input files for the Amber to run molecular dynamics (MD) simulations. This includes the following stages: minimization (min_fix.in), heating (heat_fix.in), equilibration (equ1.in to equ5.in), and production (MD1.in to MD20.in) simulations, allowing for up to 1000 ns of MD simulations for both apo proteins and ligand-protein complexes. The package also contains the MD job run script and tleap script for preparing solvated system. Gromac_plumed_input.zip: The Gromac_plumed_input package provides a suite of input files specifically designed for Gromacs simulations coupled with Plumed. It includes essential input files for various steps, such as minimization(minimization.mdp), NVT (constant number of particles, volume, and temperature) equilibration, NPT (constant number of particles, pressure, and temperature) equilibration (equilibration.mdp &equilibration_2.mdp), and production simulations (dynamic.mdp), extending up to 600 ns. Each step has the corresponding tpr file, while the Plumed simulations utilize the plumed.dat file as the input for conducting well-tempered metadynamics (WTE-metad) simulations to 1 microsecond. Also, it contains gromacs topology and coordinate files (.gro & .top) for each system. Plumed_out.zip: Plumed_out folder includes HILLS files generated from plumed.dat and used for identifying basins and drawing the free energy landscapes in each system.
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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.194 | 0.033 |
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".