| --- |
| license: other |
| tags: |
| - molecular-dynamics |
| - protein-peptide |
| - protein-structure |
| - mdm2 |
| - bioemu |
| pretty_name: MDM2 (25-109) MD, peptide complexes and BioEmu features |
| size_categories: |
| - 1K<n<10K |
| --- |
| |
| # MDM2 (25–109) — molecular dynamics, peptide complexes, and BioEmu features |
|
|
| Data for the p53-binding domain of human MDM2, residues 25–109, in the apo form |
| and in complex with peptide ligands, together with features derived from those |
| trajectories. |
|
|
| ## Contents |
|
|
| | path | what it holds | |
| |---|---| |
| | `md/p53mdm2/` | all-atom MD of MDM2(25–109) + peptide complexes | |
| | `md/mdm2_systems/` | built systems: topologies, parameters, minimised states | |
| | `md/mdm2_features/` | physical interface and receptor descriptors per frame | |
| | `md/mdm2_features_scout/` | the same descriptors on the scouting subset | |
| | `md/mdm2_joint/` | joint receptor + interface feature stores | |
| | `md/mdm2_smoke/`, `md/mdm2_test/`, `md/mdm2_buildtest/` | small build- and run-validation sets | |
| | `bioemu/mdm2_raw/` | BioEmu generative apo ensembles for MDM2(25–109) | |
| | `bioemu_l1/` | BioEmu encoder layer-1 activations on real MD frames | |
|
|
| Each folder carries its own README where the format needs one; `bioemu_l1/` |
| documents its extraction contract, its validation and its caveats in full. |
|
|
| ## The receptor sequence |
|
|
| MDM2 residues 25–109, 85 residues, chain 0 throughout: |
|
|
| ``` |
| ETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVK |
| ``` |
|
|
| ## Two things to know before using any of it |
|
|
| 1. **BioEmu features are receptor-only.** BioEmu is a monomer model. Where a |
| peptide is present in the MD that produced a conformation, it is not encoded. |
| These are MDM2 conformational features sampled along complex dynamics, not |
| joint complex embeddings. |
|
|
| 2. **A generative ensemble is not a trajectory.** Sample order in |
| `bioemu/mdm2_raw/` is not time, and no quantity derived from it is a kinetic |
| observable. |
|
|
| ## Provenance of the complex trajectories |
|
|
| The MDM2 + PMI (`TSFAEYWNLLSP`) trajectories originate from the deposit of |
|
|
| > Paul, Wehmeyer, Abualrous, Wu, Crabtree, Schöneberg, Clarke, Freund, Weikl, |
| > Noé. *Protein-peptide association kinetics beyond the seconds timescale from |
| > atomistic simulations.* Nat. Commun. **8**, 1095 (2017). |
|
|
| Redistributed under the original depositors' terms; see that paper's data |
| availability statement. |
|
|
