Data from simulations of mutations of tryptophan synthase
Bibliographic record
Abstract
Data from the article "A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the DynamicBehavior of the Catalytic Site of the Tryptophan Synthase", A. Roy and M. Karttunen J. Chem. Inf. Model. (in press (2024) Web: https://doi.org/10.1021/acs.jcim.3c01966 Preprint: https://doi.org/10.26434/chemrxiv-2023-4bhpv Four systems of TS (Tryptophan Synthase): System = Denoted by E(PLP) = e-plp E(AEX1) = e-aex1 E(AA) = e-aa E(c3) = e-c3 Each system has 3 versions: wt = WildType ala114 = mutated version (Gln114 mutated to Ala114) asn114 = mutated version (Gln114 mutated to Asn114) Folder names: 1_E(PLP) System Folders 1_wt-e-plp 2_ala114-e-plp 3_asn114-e-plp 2_E(AEX1) System Folders 4_wt-e-aex1 5_ala114-e-aex1 6_asn114-e-aex1 3_E(AA) System Folders 7_wt-e-aa 8_ala114-e-aa 9_asn114-e-aa 4_E(c3) System Folders 10_wt-e-c3 11_ala114-e-c3 12_asn114-e-c3 File names: Each folder contains AMBER readable topology, restart, input files, and also last frame pdb file: initial system topology = system.parm7 initial restart file = system.rst7 minimization 1 input file = min.in minimization 1 restart file = min.rst7 minimization 2 input file = min-all.in minimization 2 restart file = min-all.rst7 heating input file = heat.in heating restart file = heat.rst7 equilibration input file = equil.in equilibration restart file = equil.rst7 production 1 input file = md.in production 1 restart file = md.rst7 production 2 input file = md2.in production 2 restart file = md2.rst7 last frame of production = frame40000_800ns.pdb
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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 | 0.003 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.018 | 0.003 |
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".