Vina: Difference between revisions
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[[File:Screenshot from 2025-01-19 07-52-39.png|thumb|right|The residue interaction histogram.]] | [[File:Screenshot from 2025-01-19 07-52-39.png|thumb|right|The residue interaction histogram.]] | ||
This plugin enables virtual screening with the AutoDock Vina software stack. It uses Meeko and Scrubber to prepare molecular ligands, and PLIP and Matplotlib to analyze the results. | This plugin enables virtual screening with the AutoDock Vina software stack. It uses Meeko and Scrubber to prepare the target receptor and molecular ligands, and PLIP and Matplotlib to analyze the results. | ||
It was tested on PyMOL 3.1 with Python 3.10. Currently supports only Linux and probably Mac. | It was tested on PyMOL 3.1 with Python 3.10. Currently supports only Linux and probably Mac. | ||
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Cc1nc(NCc2ccccc2)c2cc[nH]c2n1 ZINC000000002036 | Cc1nc(NCc2ccccc2)c2cc[nH]c2n1 ZINC000000002036 | ||
'''Note''': Stored libraries includes the protonation state. Using such libraries means the same hydrogens are used, ignoring the chosen pH. | |||
= Guided interface = | = Guided interface = | ||
Revision as of 06:24, 29 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 virtual screening with the AutoDock Vina software stack. It uses Meeko and Scrubber to prepare the target receptor and molecular ligands, and PLIP and Matplotlib to analyze the results.
It was tested on PyMOL 3.1 with Python 3.10. Currently supports only Linux and probably Mac.
Input
Supports multi-SMILES (e.g. mols.smi), SDF and MOL files. Make sure to store your chemical libraries so it can be reused.
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
Note: Stored libraries includes the protonation state. Using such libraries means the same hydrogens are used, ignoring the chosen pH.
Guided interface
- Preparing step: Should fill the target receptor and box center selections like presented on picture. Shold also fill the the input file and output folder.
- Analyzing step: View screening results.
- Affinity list: Check the affinity of generated poses.
- Residues tree and Histogram: Check the interacting residues of generated poses (intensive computation).
- Dendogram: Check the euclidean distances of generated poses interacting residues (intensive computation).
.
Caveats
It requires internet access on plugin installation and may take time while PyMOL is freezed. Docking is as fast as base programs, but PLIP and intensive analyses are slow.
Author
Pedro Sousa Lacerda, Universidade Federal da Bahia, <pslacerda@gmail.com>.