How to Use Mol-1

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Structure Prediction & Folding Co-Folding Nucleotides Protein Folding Proteins Protein–Ligand Docking Protein–Protein Docking Small Molecules

Predict biomolecular assemblies with Mol-1

Mol-1 is an all-atom biomolecular structure predictor derived from Protenix. Submit proteins, nucleic acids, ligands, and modified residues together to model one assembly. The initial service ceiling is 1,500 tokens, counting standard residues individually and ligand or modified-residue heavy atoms individually.

How Mol-1 Works

Mol-1 samples structures with a diffusion model and ranks them by its native confidence score. Protein MSAs are generated by Neurosnap's private pipeline and supplied as unpaired alignments. Single-sequence mode disables MSAs. This version does not search for templates or RNA MSAs. Covalent-bond inputs follow Mol-1's documented restrictions; arbitrary polymer–polymer bonds are not reliably modeled.

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 Mol-1 on Neurosnap

Using Mol-1 on Neurosnap could drastically accelerate all-atom biomolecular assembly modeling.

  • Mixed assemblies: Model proteins, nucleic acids, and ligands together.
  • Confidence review: Inspect local and interface confidence alongside ranked structures.

How to Use Mol-1 on Neurosnap

To harness the capabilities of Mol-1, researchers can follow this streamlined workflow within Neurosnap:

  1. Access Neurosnap: Start by logging in to the Neurosnap website.
  2. Select Tool: From the list of available tools, choose Mol-1.
  3. Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
  4. Run Tool: Submit the Mol-1 job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
  5. 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 Mol-1 in publications or research outputs.

Molence Bio. Mol-1: Open Frontier Biomolecular Intelligence. https://github.com/molence/Mol-1.

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

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