bioemu

What problem does it solve?

BioEmu enables sampling an ensemble of backbone conformations for a protein monomer from its sequence, delivering an ensemble instead of a single predicted structure, at a fraction of MD cost.

Core Features & Use Cases

• Ensemble sampling of monomer backbones with optional steering (SMC/FKC) to improve realism or target a collective variable; side-chain reconstruction via HPacker; optional short MD relaxation; and file outputs that support downstream analysis.
• Use cases include exploring cryptic pockets, estimating folding/free-energy landscapes (ΔG_fold), and performing conformational analyses to guide design and validation workflows.
• Compatible with Bring-Your-Own-MSA or standard ColabFold embedding pipelines, with resumable sampling and steerable configurations for reproducibility.

Quick Start

Run a quick test by sampling a small ensemble from a sequence using a modest number of samples and inspect the topology.pdb and samples.xtc outputs.