PocketXMol | Small Molecule Design
Pocket-conditioned small-molecule generation and fragment expansion.
Overview
PocketXMol Small Molecule Design is the structure-based drug-design PocketXMol workflow for generating or expanding small molecules inside a receptor pocket. It supports both de novo pocket-conditioned generation and fragment-based design workflows such as fragment growing and fragment linking.
Run PocketXMol | Small Molecule Design on Neurosnap
The PocketXMol | Small Molecule Design online webserver allows anybody with a Neurosnap account to run and access PocketXMol | Small Molecule Design, 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
- Supports de novo structure-based small-molecule generation from a receptor pocket.
- Supports fragment growing from a user-specified seed molecule.
- Supports fragment linking from multiple user-specified fragment groups.
- Uses pocket-conditioned 3D generation rather than only sequence- or string-based chemistry priors.
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 | Small Molecule Design 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 | Small Molecule Design 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/ |