| _version_ | 1866902225470619648 |
|---|---|
| author | Polishchuk, Pavel |
| author_facet | Polishchuk, Pavel |
| contents | <p>This is an apptainer image to predict protonation states of small molecules be means of Uni-pKa. It was developed to integrate Uni-pKa model into the autiomated docking pipeline provided by <a href="https://github.com/ci-lab-cz/easydock" target="_blank" rel="noopener">EasyDock</a>.</p> <p>To run predictions outside of EasyDock you may use the command</p> <p><code>apptainer run unipka.sif protonate -i input.smi -o output.smi</code></p> <p>It may be necessaru to mount directories where input and output files are located. Use argument <code>-B /path/to/dir</code></p> <p>The script will use GPU if it will be detected in a system.</p> <p>To make prediction for different pH, change the argument <code>--pH</code></p> <p><code>apptainer run unipka.sif protonate -i input.smi -o output.smi --pH 8</code></p> <p> </p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17506578 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Uni-pKa protonation container Polishchuk, Pavel <p>This is an apptainer image to predict protonation states of small molecules be means of Uni-pKa. It was developed to integrate Uni-pKa model into the autiomated docking pipeline provided by <a href="https://github.com/ci-lab-cz/easydock" target="_blank" rel="noopener">EasyDock</a>.</p> <p>To run predictions outside of EasyDock you may use the command</p> <p><code>apptainer run unipka.sif protonate -i input.smi -o output.smi</code></p> <p>It may be necessaru to mount directories where input and output files are located. Use argument <code>-B /path/to/dir</code></p> <p>The script will use GPU if it will be detected in a system.</p> <p>To make prediction for different pH, change the argument <code>--pH</code></p> <p><code>apptainer run unipka.sif protonate -i input.smi -o output.smi --pH 8</code></p> <p> </p> |
| title | Uni-pKa protonation container |
| url | https://doi.org/10.5281/zenodo.17506578 |