How to use BioEmu2 Online

Predict structures and sample biomolecular dynamics with BioEmu2 online.

BioEmu2 is a generative model for biomolecular structure and dynamics from Microsoft Research AI for Science. It supports proteins, nucleic acids, and small molecules. Choose Structure Prediction for folded conformations, Equilibrium Sampling for an ensemble, or Time Propagation for successive time-lagged transitions from a complete mmCIF structure.

How BioEmu2 Works

Provide sequences and optional noncovalent molecules, or import composition from an mmCIF with complete entity metadata. Time Propagation also requires complete starting coordinates. Set the conformation count for independent sampling, or the time lag and propagation steps for dynamics. Review the trajectory and per-frame table; equilibrium and prediction frames are independent samples, not time-ordered trajectories. RMSD is fitted to the first frame over all heavy atoms. Protein geometry checks flag potentially implausible frames without removing them and do not validate nucleic acids or ligands. No confidence ranking is inferred. Explicit covalent bonds, branched polymers, custom restraints, steering, and multi-GPU sampling are not exposed in this integration.

What is Neurosnap?

Neurosnap is the leading platform for bioinformatics and computational science focused on expanding access to powerful modeling and simulation tools. Because many state-of-the-art machine learning systems remain complex to install, configure, and scale, Neurosnap offers a clean, browser-based workspace that removes the burden of infrastructure management, dependency conflicts, and command-line tooling.

Built for biologists, chemists, and cross-disciplinary scientists, the platform enables advanced computational workflows without requiring expertise in software engineering or cloud architecture. Researchers can launch analyses through an intuitive interface, connect programmatically through a comprehensive API, and rely on automated resource management to scale workloads efficiently. By taking care of the underlying compute and operational complexity, Neurosnap allows teams to devote their energy to scientific progress and faster iteration. Security and data protection remain foundational principles, with clear safeguards outlined in our Terms of Use and Privacy Policy to ensure your work stays protected.

Advancing Discovery with BioEmu2 on Neurosnap

Using BioEmu2 on Neurosnap could drastically accelerate biomolecular structure prediction, equilibrium sampling, and time-lagged conformational exploration.

Generate multiple conformations of a complex.
Explore time-lagged transitions from complete starting coordinates.
Inspect trajectory playback alongside per-frame geometry checks.

How to Use BioEmu2 on Neurosnap

To harness the capabilities of BioEmu2, researchers can follow this streamlined workflow within Neurosnap:

Access Neurosnap: Start by logging in to the Neurosnap website.
Select Tool: From the list of available tools, choose BioEmu2.
Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
Run Tool: Submit the BioEmu2 job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
Review Output: Explore your results through rich visualizations, including figures, plots, and interactive views designed to help you analyze findings with clarity and confidence.

Citations

Please cite the original work when using BioEmu2 in publications or research outputs.

Microsoft Research AI for Science. BioEmu2. https://github.com/microsoft/bioemu2

Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/

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