OpenDDE
Open-source all-atom co-folding model for proteins, nucleic acids, ligands, and ions.
Overview
OpenDDE is an open-source, all-atom biomolecular foundation model for co-folding proteins, nucleic acids, ligands, and ions. It uses an AlphaFold3-style JSON input format and returns ranked structures with confidence summaries for complex structure prediction and drug-discovery modeling workflows.
Run OpenDDE on Neurosnap
The OpenDDE online webserver allows anybody with a Neurosnap account to run and access OpenDDE, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- All-atom co-folding for mixed biomolecular systems.
- Supports proteins, DNA, RNA, ligands, and ions in one prediction job.
- Provides ranked mmCIF structures with confidence-summary outputs.
- Includes a general-purpose checkpoint and an antibody-antigen checkpoint option.
- Can run MSA-free for faster compatibility-oriented predictions.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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| Credit Usage Rate | loading... |
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| Runtime Mean | loading... |
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| Runtime Standard Deviation | loading... |
| Runtime 90th Percentile | loading... |
| Runtime Longest | loading... |
API Request
Access OpenDDE using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using OpenDDE in publications or research outputs.
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Aureka AI Research. OpenDDE: An Open-source Drug Discovery Engine. arXiv:2607.03787 (2026). |
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Aureka AI Research. OpenDDE GitHub repository. https://github.com/aurekaresearch/OpenDDE |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |