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 running step.

The analyzing step.

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.

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

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.
• Running step: Follow the graphical interface to go over this step.
• Analyzing step: View screening results.
  • Affinity list: Check the affinity of generated poses.
  • Residues tree and Histogram: Check the interacting residues of generated poses (intense computation).
  • Dendogram: Check the euclidean distances of generated poses interacting residues (intense 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>.