README.md

metadata

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.