Vina: Difference between revisions
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It is free software. | It is free software. | ||
= Input = | |||
Multi-smi SMILES file (e.g. ''mols.smi''). | Multi-smi SMILES file (e.g. ''mols.smi''). | ||
| Line 26: | Line 26: | ||
Cc1nc(NCc2ccccc2)c2cc[nH]c2n1 ZINC000000002036 | 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. | * '''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. | * '''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. | ||
= Author = | |||
Pedro Sousa Lacerda. | Pedro Sousa Lacerda. | ||
Revision as of 17:40, 17 January 2025
| Type | PyMOL Plugin |
|---|---|
| Download | https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/plugins/vina.py |
| Author(s) | Pedro Sousa Lacerda |
| License | Free Software |
Vina (vs.py)
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.
It is free software.
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.
Author
Pedro Sousa Lacerda.