Vina: Difference between revisions

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= Input =
= Input =


Supports only multi-smi SMILES files (e.g. ''mols.smi''). Make sure to store your chemical libraries so it can be reused.
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
     Cc1c(Cl)cccc1Nc1ncccc1C(=O)OC[C@H](O)CO ZINC000000000171
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= Guided interface =
= 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''. The ''flexible'' selection is optional.
* '''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.
* '''Running step''': Follow the graphical interface to go over this step.
* '''Analyzing step:''' View screening results.
* '''Analyzing step''': View screening results.
** '''PLIP:''' Check the generated molecular interaction poses.
** '''Affinity list''': Check the affinity of generated poses.
** '''Histogram:''' Check interacting residues within the chemical library.
** '''Residues tree''' and '''Histogram''': Check the interacting residues of generated poses (''intensive'').
** '''Dendogram''': Check the euclidean distances of generated poses (''intensive'').
 
.
= Caveats =
= 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 chart analyses are slow.
 
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 =
= Author =


Pedro Sousa Lacerda <pslacerda@gmail.com>.
Pedro Sousa Lacerda, Universidade Federal da Bahia, <pslacerda@gmail.com>.
 
Universidade Federal da Bahia.

Revision as of 21:53, 25 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
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 (intensive).
    • Dendogram: Check the euclidean distances of generated poses (intensive).

.

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>.

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