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
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.
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.
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