BioEmu

Overview

Exploring domain motion, local unfolding, or cryptic-pocket hypotheses.
Generating diverse starting conformations for downstream inspection.
Comparing variant ensembles under matched sampling settings.

Modes

Mode	Input shape	When to use it
`sampling` Sample Ensemble Default	Uses one selected file/source when file parameters are present.	Generate a conformational ensemble from an A3M alignment.

Canonical Job Configuration

These are the fields exposed by the default job configuration for bioemu. They are also returned by GET /api/v1/program/params?program=bioemu and submitted as the params JSON object to POST /api/v1/job/submit.

Parameter	Type	Modes	What it does
`alignment_file` A3M Alignment	MSA file	All modes	Choose an A3M file with the query sequence as the first row. Required; Files: .a3m
`sample_count` Samples	Integer	All modes	Number of conformational samples to generate before optional physical filtering. Default: 100; Range: 1-10000
`keep_only_physical` Keep Only Physical Samples	Yes/no	All modes	Filter chain breaks and steric clashes from the final PDB/XTC outputs. Default: true
`steering_strength` Physical Steering	Text	All modes	Optional sampling guidance to reduce chain breaks and steric clashes; stronger settings cost more runtime. Default: Off; Options: Off, Light, Standard, Strong
`atom_detail` Atom Detail	Text	All modes	Backbone trajectory keeps the native BioEmu outputs; all-heavy-atom also reconstructs side chains after sampling. Default: All-heavy-atom trajectory; Options: Backbone trajectory, All-heavy-atom trajectory
`run_md_equilibration` Run MD Equilibration	Yes/no	All modes	After side-chain reconstruction, run OpenMM local minimization/equilibration. Default: false; Shown when atom_detail is All-heavy-atom trajectory
`md_protocol` MD Protocol	Text	All modes	Local minimization is faster; MD equilibration adds a short constrained equilibration stage. Default: local_minimization; Options: local_minimization, md_equil; Shown when run_md_equilibration is true

Advanced configuration fields

Parameter	Type	Modes	What it does
`simulation_time_ns` Free MD Time (ns)	Number	All modes	Optional unconstrained MD after equilibration; 0 disables the free MD run. Default: 0; Range: 0-1; Shown when run_md_equilibration is true
`random_seed` Random Seed	Integer	All modes	Set for reproducible sampling; leave blank for a random seed. Range: 1-999999999

Outputs And Metrics

Topology PDB, trajectory files, sequence FASTA, and raw coordinate batches.
All-heavy-atom runs can include side-chain reconstructed structures and trajectories.
MD-equilibrated runs can include additional equilibrated structure and trajectory files.
BioEmu does not automatically compute RMSD, clustering, free-energy, or representative-frame metrics; analyze the ensemble downstream.

Common Examples

Quick exploration: 100 samples, physical filtering on, backbone trajectory.
Cleaner inspection ensemble: 500-1000 samples, standard steering, all-heavy-atom output.
Variant comparison: keep sample count, steering, atom detail, and seed matched across variants.

Example API params

{
  "mode": "sampling",
  "alignment_file": "target.a3m",
  "sample_count": 100,
  "keep_only_physical": true,
  "atom_detail": "Backbone trajectory"
}

Caveats

BioEmu is intended for monomer ensembles, not complexes, ligands, or sequence generation.
Side chains are reconstructed after backbone sampling; inspect contacts before using side-chain interactions for binding interpretations.
Filtering can reduce the final number of retained samples.

Advanced Submit

Advanced submit is still available for direct program arguments through POST /api/v1/job/submit-advanced. Prefer canonical configuration unless you need exact low-level arguments or are reproducing a known command line.

Advanced submit accepts BioEmu command lines for specialized sampling and post-processing choices.
Keep A3M inputs well formed with the query sequence as the first record.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=bioemu \
  -F 'params={"mode":"sample_ensemble","a3m_file":"target.a3m","samples":100,"keep_physical":true,"atom_detail":"Backbone trajectory"}'