Vina: Difference between revisions
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{{Infobox script-repo | {{Infobox script-repo | ||
|type = plugin | |type = plugin | ||
|download = https:// | |download = https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/refs/heads/master/plugins/vina.py | ||
|author = Pedro Sousa Lacerda | |author = Pedro Sousa Lacerda | ||
|license = Free Software | |license = Free Software | ||
| Line 26: | Line 26: | ||
* '''Running step.''' Follow the graphical interface to go over this step. | * '''Running step.''' Follow the graphical interface to go over this step. | ||
* '''Analyzing step.''' Check the molecular generated interaction poses. | * '''Analyzing step.''' Check the molecular generated interaction poses. | ||
= Caveats = | |||
It requires internet access on plugin installation and may take time. | |||
= Author = | = Author = | ||
Pedro Sousa Lacerda. | Pedro Sousa Lacerda. | ||
Revision as of 19:55, 17 January 2025
| Type | PyMOL Plugin |
|---|---|
| Download | https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/refs/heads/master/plugins/vina.py |
| Author(s) | Pedro Sousa Lacerda |
| License | Free Software |
This plugin enables small scale virtual screening with the AutoDock Vina software stack. It uses Meeko and Scrubber to prepare molecular ligands, and PLIP to analyze the results.
It was tested on PyMOL 3.0 with Python 3.10. Currently supports only Linux and probably Mac.
Input
Multi-smi SMILES file (e.g. mols.smi).
Cc1c(Cl)cccc1Nc1ncccc1C(=O)OC[C@H](O)CO ZINC000000000171 CN(C)CC[C@@H]1c2ccc(Cl)cc2CCc2cccnc21 ZINC000000000179 CC(C)NC[C@H]1CCc2cc(CO)c([N+](=O)[O-])cc2N1 ZINC000000000570 Cc1nc(NCc2ccccc2)c2cc[nH]c2n1 ZINC000000002036
Guided interface
- Preparing step. While on the preparation step, should fill the target receptor and box center selections like presented on picture. Shold also fill the the input file and output folder. The flexible selection is optional.
- Running step. Follow the graphical interface to go over this step.
- Analyzing step. Check the molecular generated interaction poses.
Caveats
It requires internet access on plugin installation and may take time.
Author
Pedro Sousa Lacerda.