Martini 3 force field parameters for protein lipidation post-translational modifications
Bibliographic record
Abstract
Data for the publication "Martini 3 force field parameters for protein lipidation post-translational modifications" in the Journal of Chemical Theory and Computation Protein lipidations are vital co-translational or post-translational modifications that tether lipid tails to specific protein aminoacids to allow them to anchor to biological membranes, switch their subcellular localizations, and modulate association with other proteins. Such lipidations are thus crucial for multiple biological processes such as signal transduction, protein trafficking and membrane localization, and are implicated in various diseases as well. Examples of such lipid-anchored proteins include the Ras family of proteins that undergo farnesylation, actin and gelsolin, which are myristoylated, phospholipase D, which is palmitoylated, glycosylphosphatidylinositol-anchored proteins and others. Here, we develop parameters for the latest version of the Martini 3 coarse-grained force field for cysteine-targeting farnesylation, geranylgeranylation and palmitoylation as well as the glycine-targeting myristoylation due to the importance of these lipidations in disease and in particular for studying cancer and anti-cancer drug discovery. The parameters are developed using the CHARMM36m all-atom force field parameters as reference. The behavior of the coarse-grained models is consistent with that of the all-atom force field for all lipidations and reproduces key dynamical and structural features such as solvent-accessible surface area, bilayer penetration depth, and cluster representative conformations. The parameters, along with mapping schemes for the popular martinize2 tool, are immediately available for download.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| 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".