Vina

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

The preparation step.

The execution log.

The analyzing step.

The residue interaction histogram.

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 on Fedora Linux 41, but Windows is partially supported and maybe Mac also works.

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 results

The top max load conformations ranked up to max mode are listed on the interface. Click on the molecule name (suffix _m5 denotes the fifth model) to render a PLIP visualization of the docked ligand. Click on the export table to save the loaded molecule's affinity into a XLSX file.

If the Intensive computation is enabled, the plugin will compute the PLIP interaction for loaded poses and plot an AuPosSOM-like dendogram tree based on pose similarity. A bar chart counting the number of interactions the residue does for each PLIP interaction type

Instalation

Install using the URL on the Plugin Manager, it should be straightforward with automatic dependencies install.

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>.