Useful links
| Tool | Description |
|---|---|
| IDP-ELM | Our work Intrinsically disordered protein prediction |
| pKALM | Our work Protein pKa values from amino acid sequences |
| DeepKa | Protein pKa prediction server; predict from structures |
| COBALT | Multiple sequence alignment |
| IQ-TREE | Phylogenetics inference |
| PsiPartition | Our work Partitioned models for phylogenomics |
| PatchDock | Protein docking server; Fast; require only pdb files |
| OpenBabel | Swiss army knife for format conversion of chemical files |
| AutoDock | Protein docking software |
| Uni-Dock | Protein docking software; Very fast; GPU-accelerated |
| PyMOL | Protein visualization software |
| GIMP | Image editing software |
| Blender | 3D modeling software |
| LaTeX | Paper writing & presentation tool |
A Simple Tutorial for AutoDock Vina
This is a simple tutorial for using AutoDock Vina. The Auto Dock softwares are available at their official website. However, DO NOT install the binaries downloaded there because they are outdated and may not work properly. Please follow the instructions below to run a simple protein-ligand docking using AutoDock Vina:
- Download the latest version of AutoDock Vina from here.
For Windows please download two *.exe files. For Linux and MacOS users, download the corresponding files. Note that "x86_64" means Intel or AMD chips while "aarch" means ARM chips. It is important to download the "mac_aarch" version for Macbook M1/M2/M3 chips. - Download the OpenBabel software from here. Choose "x64" version (unless your PC is very old and is 32-bit), download the corresponding *.exe file. Please also install openbabel for other operating systems. Install OpenBabel by double-clicking the downloaded file on Windows.
- Prepapre the protein receptor and ligand files in pdb format. In this tutorial, I will use myoglobin (PDB ID: 5MBA) and heme as an example. Download myoglobin and heme. Put them in the same directory where you put the AutoDock Vina files:
- Open a terminal and navigate to the directory where you extracted the files. On Windows you can search PowerShell in start menu. On Linux and MacOS please open the Terminal.
- Run the following commands to convert pdb files to pdbqt files:
Now you should have two new files: rec.pdbqt and heme.pdbqt:obabel -ipdb rec.pdb -xrp -O rec.pdbqt obabel -ipdb heme.pdb -O heme.pdbqt
- Now you can run the software by typing following command in the terminal:
Note here you need to provide the coordinates of the center and the size of the grid box. I write a simple Python sciprt to calculate the center and size of the grid box. You can download the script here. And the outputs should be like this:./vina_1.2.5_win.exe --receptor .\rec.pdbqt --ligand .\heme.pdbqt --center_x -56.1875 --center_y -43.975998 --center_z -29.534 --size_x 38.026997 --size_y 37.104 --size_z 36.211998 --exhaustiveness 32 --out results.out
- After the calculation is done, you can find the results in the file "results.out". The file contains several docking poses, which need to be split. Type the following command to split the file:
and this will generate several pdbqt files: results.out_ligand_[1-10].pdbqt. Drag all of them, as well as the receptor file, to PyMOL to visualize the results../vina_split_1.2.5_win.exe --input .\results.out
