Use OpenFE Absolute Binding Free Energy
Official Neurosnap webserver for accessing OpenFE Absolute Binding Free Energy online.
Overview
Compute an absolute protein-ligand binding free energy with the OpenFE framework from a prepared protein structure and one positioned SDF ligand.
Neurosnap Overview
The OpenFE Absolute Binding Free Energy online webserver allows anybody with a Neurosnap account to run and access OpenFE Absolute Binding Free Energy, 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
- Runs absolute binding free energy calculations with OpenFE on CUDA GPUs.
- Retains the protein-relative coordinates and bond orders from the uploaded SDF ligand.
- Uses automatic Boresch restraints and rigorous MBAR analysis.
- Supports OpenFF Sage or GAFF2 ligand parameters with AMBER ff14SB for the protein.
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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API Request
Access OpenFE Absolute Binding Free Energy 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 OpenFE Absolute Binding Free Energy in publications or research outputs.
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Alibay, I. et al. The Open Free Energy library. Zenodo, 2025. https://doi.org/10.5281/zenodo.8344247. |
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Eastman, P. et al. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLOS Computational Biology, 2017. https://doi.org/10.1371/journal.pcbi.1005659. |
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Shirts, M.R. & Chodera, J.D. Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics, 2008. https://doi.org/10.1063/1.2978177. |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |
Job Note
Provide a name or description for your job to help you organize and track its results. This input is solely for organizational purposes and does not impact the outcome of the job.
Inputs & Configuration
Ready to submit your job?
Review your configuration, then confirm the estimated credit cost before you run the job.
Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: calculating...
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