PocketXMol | Dock
Pocket-conditioned docking for small molecules or peptides.
Overview
PocketXMol Dock is the docking-focused PocketXMol workflow for placing either a small molecule or a peptide into a protein binding pocket. It uses the same pocket-conditioned three-dimensional modeling framework as the broader PocketXMol family, but the service is scoped specifically to receptor-guided docking rather than open-ended design.
Run PocketXMol | Dock on Neurosnap
The PocketXMol | Dock online webserver allows anybody with a Neurosnap account to run and access PocketXMol | Dock, 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
- Handles both small-molecule and peptide docking against a protein pocket.
- Uses a pocket-conditioned 3D interaction model rather than a purely ligand-only prior.
- Accepts either an explicit pocket reference or a user-defined pocket center override.
- Returns docked structural proposals suitable for downstream review or rescoring.
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 PocketXMol | Dock 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 PocketXMol | Dock in publications or research outputs.
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Peng, X., Guo, R., Guo, F., Wang, Z., Sun, J., Guan, J., Jia, Y., Xu, Y., Huang, Y., Zhang, M., Peng, J., Wang, X., Han, C., Wang, Z., and Ma, J. Unified modeling of 3D molecular generation via atomic interactions with PocketXMol. Cell (2026). https://doi.org/10.1016/j.cell.2026.01.003 |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |