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 | This plugin enables virtual screening with the AutoDock Vina software stack. It uses Meeko and Scrub 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. | ||
| Line 18: | Line 18: | ||
= Input = | = Input = | ||
Supports multi-SMILES | Supports multi-SMILES, SDF and MOL files, the same formats supported by Scrub. Make sure to store your chemical libraries so it can be reused. The snippet below illustrate a SMILES file with multiple SMILES separated from the molecule name by empty spaces. | ||
Cc1c(Cl)cccc1Nc1ncccc1C(=O)OC[C@H](O)CO ZINC000000000171 | Cc1c(Cl)cccc1Nc1ncccc1C(=O)OC[C@H](O)CO ZINC000000000171 | ||
| Line 25: | Line 25: | ||
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 | '''Note''': Stored libraries includes the protonation state. Using such libraries means the same hydrogens are used, ignoring the specified pH. | ||
= | = Usage = | ||
; Run docking/screening | |||
: Fill the ''target receptor'' and ''box center'' with . They must be selections or objects or extracted objects already loaded into PyMOL. If there are rigid ligands (e.g. a cofactor) or important water molecules, they must be on the ''receptor'' selection/object. Click on ''Run'' to start. | |||
* '''Analyzing step''': View screening results. | * '''Analyzing step''': View screening results. | ||
** '''Affinity list''': Check the affinity of generated poses. | ** '''Affinity list''': Check the affinity of generated poses. | ||
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** '''Dendogram''': Check the euclidean distances of generated poses interacting residues (''intensive computation''). | ** '''Dendogram''': Check the euclidean distances of generated poses interacting residues (''intensive computation''). | ||
. | . | ||
= Instalation = | |||
Install using the URL on the Plugin Manager. On the first time executing the plugin, it may freeze PyMOL while downloading the required Python packages (libraries). In case of <code>ImportError</code> messages, it's recommended to troubleshot the following commands on the PyMOL console. | |||
conda install -y matplotlib openpyxl scipy meeko plip openbabel rdkit pandas lxml | |||
pip install https://github.com/pslacerda/molscrub/archive/refs/heads/windows.exe.zip | |||
The general syntax is run <code>conda install -y</code> or <code>pip install</code> prefixing the wanted/required package. | |||
= Caveats = | = Caveats = | ||
The main docking or screening step is as fast as base programs, but the analyze interface is slow, specially if the "intensive" computation option is enabled. | |||
= Author = | = Author = | ||
zzPedro Sousa Lacerda, Universidade Federal da Bahia, <pslacerda@gmail.com>. | |||
Revision as of 03:11, 6 February 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 Scrub 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, SDF and MOL files, the same formats supported by Scrub. Make sure to store your chemical libraries so it can be reused. The snippet below illustrate a SMILES file with multiple SMILES separated from the molecule name by empty spaces.
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 specified pH.
Usage
- Run docking/screening
- Fill the target receptor and box center with . They must be selections or objects or extracted objects already loaded into PyMOL. If there are rigid ligands (e.g. a cofactor) or important water molecules, they must be on the receptor selection/object. Click on Run to start.
- 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).
.
Instalation
Install using the URL on the Plugin Manager. On the first time executing the plugin, it may freeze PyMOL while downloading the required Python packages (libraries). In case of ImportError messages, it's recommended to troubleshot the following commands on the PyMOL console.
conda install -y matplotlib openpyxl scipy meeko plip openbabel rdkit pandas lxml pip install https://github.com/pslacerda/molscrub/archive/refs/heads/windows.exe.zip
The general syntax is run conda install -y or pip install prefixing the wanted/required package.
Caveats
The main docking or screening step is as fast as base programs, but the analyze interface is slow, specially if the "intensive" computation option is enabled.
Author
zzPedro Sousa Lacerda, Universidade Federal da Bahia, <pslacerda@gmail.com>.