Published June 16, 2025 | Version v1
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Supplementary data for "scalable emulation of protein equilibrium ensembles with generative deep learning"

Authors/Creators

  • 1. Microsoft Research
  • 2. ROR icon Freie Universität Berlin

Description

Supplementary data for Biomolecular Emulator

Overview

This repository contains supplementary data for Biomolecular Emulator:

Lewis, S.; Hempel, T.; Jiménez-Luna, J.; Gastegger, M.; Xie, Y.; Foong, A. Y. K.; Satorras, V. G.; Abdin, O.; Veeling, B. S.; Zaporozhets, I.; Chen, Y.; Yang, S.; Foster, A. E.; Schneuing, A.; Nigam, J.; Barbero, F.; Stimper, V.; Campbell, A.; Yim, J.; Lienen, M.; Shi, Y.; Zheng, S.; Schulz, H.; Munir, U.; Sordillo, R.; Tomioka, R.; Clementi, C.; Noé, F. Scalable Emulation of Protein Equilibrium Ensembles with Generative Deep Learning. Science 2025. https://doi.org/10.1126/science.adv9817.
 

Supplementary code

This repository contains a snapshot of the bioemu inference and benchmark code,

We strongly recommend using the linked GitHub repositories for up-to-date code, installation instructions, and further information. This Zenodo repository represents a static snapshot of supplementary data for the publication.

The code is licensed under the MIT License.
 

Model checkpoints

The model checkpoints that were used to produce the results for the publication are given in
  • bioemu_finetuned_step_4421376000_epoch_00100.ckpt: Default BioEmu model used throughout the publication
  • desres-models.zip: fast folder model, Fig. 3 A (for developers, please do not use for inference unless explicitly intended)
The model checkpoints are licensed under the MIT License.
 

Supplementary structures

This repository contains the molecular structures that were used to generate the results in the above publication.

The supplementary structures are licensed under Community Data License Agreement - Permissive - Version 2.0.

Figure panel data assignment:

The samples_*.zip files map to the paper figures as follows:

  • samples_cath.zip: Fig. 3 B, Fig. S10 A
  • samples_cath-scaling-001.zip: Fig. 3 B; Fig. S10 C
  • samples_cath-scaling-010.zip: Fig. 3 B; Fig. S10 C
  • samples_cath-scaling-100.zip: Fig. 3 B; Fig. S10 C
  • samples_delta_G.zip: Fig. 4 B, C and F
  • samples_desres_model.zip: Fig. 3 A; Fig. S9
  • samples_e2e_multiconf_crypticpocket.zip: Fig. S6
  • samples_e2e_multiconf_domainmotion.zip: Fig. S6
  • samples_e2e_multiconf_ood60_local.zip: Fig. S6
  • samples_e2e_singleconf_localunfolding.zip: Fig. S6
  • samples_examples_fig3.zip: Fig. 3 C and D; Fig 12
  • samples_multiconf_crypticpocket.zip: Fig. 2 C; Fig. S4
  • samples_multiconf_domainmotion.zip: Fig. 2 A; Fig. S2
  • samples_multiconf_ood60_local.zip: Fig. S1
  • samples_singleconf_localunfolding.zip: Fig. 2 B; Fig. S3
  • samples_stable_proteins.zip: Fig 4 D
  • samples_unstable_proteins.zip: Fig 4 E

Data loading

The data can be loaded with common molecular dynamics tools, e.g.,
with mdtraj:

import mdtraj
samples = mdtraj.load("path/to/samples.xtc", top="path/to/topology.pdb")

Files

bioemu-benchmarks_code_release.zip

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Additional details

Software

Repository URL
https://github.com/microsoft/bioemu/

References