Docking Tutorial Using Autodock Vina version 1.2.3 (2021) and AutoDock-GPU Version 1.5.3

Video tutorials can be seen at the following link:

1. Using Autodock Vina: Part 1: https://www.youtube.com/watch?v=Xa0SxkDritI&t=614s and Part 2: https://youtu.be/L4mbxlF7Mnk
2. Using AutoDock-GPU https://youtu.be/KotAUEJTDAY

Required software

1. Vina.exe (Version 1.2.3) download here https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.3/vina_1.2.3_windows_x86_64.exe, vina_1.2.3_windows_x86_64.exe change the name to vina.exe or https://drive.google.com/file/d/1DBAsOPNDttz1ktoONc-EsCFT3IWHFjbj/view?usp=sharing
2. ADFR Tools (Version 1.2) https://ccsb.scripps.edu/adfr/download/1067/
3. Mgl Tools (Version 1.5.7) https://ccsb.scripps.edu/download/262/
4. Vina_Split https://github.com/purnawanpp/Docking-4ieh/blob/main/vina_split.exe
5. Windows terminal https://www.microsoft.com/en-us/p/windows-terminal/9n0dx20hk701
6. Avogadro (Version 1.2) https://sourceforge.net/projects/avogadro/files/latest/download
7. Discovery Studio (Version 2022) https://discover.3ds.com/discovery-studio-visualizer-download
8. Marvin Sketch https://drive.google.com/file/d/18WN28mtb_ayVKFc09CgDaI5VBJVdESm9/view?usp=sharing or website https://chemaxon.com/products/marvin/download how to install Marvin Sketch (Version 2022) how to install marvin sketch https://www.researchgate.net/profile/Purnawan-Pontana-Putra/publication/356913436_Tutorial_Installing_Marvin_Sketch_Software_and_Using_SWISS_ADME/links/61b2b2ee590a0b7ed6346b1a/Tutorial-Installing-Marvin-Sketch-Software-and-Using-SWISS-ADME.pdf

All Software Recap

1. https://drive.google.com/drive/folders/1_2wk2VlJUH8EFpytu34mPQQuF6pq4_zE?usp=sharing

Path Settings

1. Open the path, in the search field type path
2. Click Environmental Variables
3. Click Path Edit
4. Click New, enter the location of the file or folder in the path
5. Click Ok until all windows are closed (3 times click ok)
6. There are 4 things that must be entered in the path, namely:
   1. C:\Program Files (x86)\MGLTools-1.5.7,
   2. C:\Program Files (x86)\ADFRsuite-1.0\bin and the location folder
   3. vina. exe
   4. vina_split.exe

How to find out the active site and its binding site

1. Read the protein article
2. Using the Uniprot website https://www.uniprot.org/
3. Using the Discovery Studio application,
4. Using online server applications such as: ICM-PocketFinder, CASTp, Chimera, Qsite, Scfbio online server

Separation of ligands and proteins (Using Biovia Discovery Studio)

1. Separate the Protein, remove the water and the ligand
2. Separate ligands, remove protein, water

Protein Preparation (Using Autodock Tools)

1. Separate water and ligands first using Biovia Discovery Studio
2. Click File Read Molecules look for protein.pdb
3. Added Hydrogen with Edit-Add Hydrogen-All
4. Edit add gasteiger charge
5. Edit-Hydrogen Merge Non Polar
6. Grid-Macromolecules-Choose
7. save protein.pdbqt

Ligand Preparation (Using Autodock Tools)

1. Select File Read Molecules, look for ligand.pdb
2. Added Hydrogen with Edit-Add Hydrogen-All
3. Edit add gasteiger charge
4. Edit-Hydrogen Merge Non Polar
5. Ligand-Input-choose
6. Select ligand.pdb
7. ligand-Toorsion tree-detect root
8. Click Ligand-Torsion Tree-Choose Torsions, Select Done
9. Select Ligand-Torsion Tree-Set Number of Torsions select fewest atom, and Dismiss
10. Select Ligand-output-save as ligand.pdbqt

Command in terminal to find out Grid Box using Autogrid (Using Terminal)

1. python.exe prepare_gpf.py -l 4ieh_ligand.pdbqt -r 4ieh_protein.pdbqt -y
2. autogrid4 -p 4ieh_protein.gpf -l 4ieh_protein.glg

Create the GridBox File (Using Notepad), this preparation for using Autodock Vina

1. Open the file with 4ieh_protein.gpf
2. Record npts 50 40 40 as size x, y, z
3. Record gridcenter -0.004 -0.187 0.078 as center x, y, z
4. Create a grid.txt file in it that says: center_x = -0.004 center_y = -0.187 center_z = 0.078 size_x = 50 size_y = 40 size_z = 40
5. An example of a grid.txt file can be seen here https://github.com/purnawanpp/Docking-4ieh/blob/main/grid.txt

Option 1-Docking Procedure using Vina version 1.2.3 (Using Terminal)

1. vina --receptor 4ieh_protein.pdbqt --ligand 4ieh_ligand.pdbqt --config grid.txt --exhaustiveness=8 --out 4ieh_ligand_vina_out.pdbqt > results.txt
2. vina_split --input 4ieh_ligand_vina_out.pdbqt

Option 2-Docking Procedure using Autodock-GPU version 1.5.3 (Using terminal)

1. Video tutorial is here: https://youtu.be/KotAUEJTDAY
2. Upload all the prepared files
3. Run and open the following script file on google colab: https://github.com/purnawanpp/Docking-4ieh/blob/main/Autodock_GPU.ipynb
4. Download the .dlg format file and open it using Notepad++, find minimal energy with the command run =

Calculation of RMSD value (Using Biovia Discovery Studio)

1. Open the file 4ieh_ligand.pdbqt
2. Drag the file 4ieh_ligand_vina_out_ligand_1.pdbqt
3. Click File 4ieh_ligand.pdbqt,
4. Click Structure-RMSD-Set Reference
5. Click File 4ieh_ligand_vina_out_ligand_1.pdbqt
6. Click Structure-RMSD-Heavy Atoms
7. At the bottom you will see the RMSD value, the recommended RMSD value is <2

additional option prepare protein and ligand using adfr (using terminal)

1. Prepare protein: prepare_receptor -r rec.pdb -o rec.pdbqt
2. Prepare ligand: prepare_ligand -l lig.pdb -o hasil.pdbqt -U nphs_lps

Docking Tutorial Penggunaan Autodock Vina dan AutoDock-GPU (Bahasa Indonesia)

Video Tutorial dapat dilihat di link berikut:

1. Part 1: https://www.youtube.com/watch?v=Xa0SxkDritI&t=614s dan Part 2: https://youtu.be/L4mbxlF7Mnk
2. Penggunaan AutoDock-GPU https://youtu.be/KotAUEJTDAY

Semua file Perangkat lunak yang dibutuhkan download disini

1. https://drive.google.com/drive/folders/1_2wk2VlJUH8EFpytu34mPQQuF6pq4_zE?usp=sharing

Perangkat lunak yang dibutuhkan

1. Vina.exe (Version 1.2.3) download disini https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.3/vina_1.2.3_windows_x86_64.exe, vina_1.2.3_windows_x86_64.exe ubah namanya menjadi vina.exe atau download dari link berikut: https://drive.google.com/file/d/1DBAsOPNDttz1ktoONc-EsCFT3IWHFjbj/view?usp=sharing
2. ADFR Tools (Version 1.2) https://ccsb.scripps.edu/adfr/download/1067/
3. Mgl Tools (Version 1.5.7) https://ccsb.scripps.edu/download/262/
4. Vina_Split https://github.com/purnawanpp/Docking-4ieh/blob/main/vina_split.exe
5. Windows terminal https://www.microsoft.com/en-us/p/windows-terminal/9n0dx20hk701
6. Avogadro (Version 1.2) https://drive.google.com/file/d/1DzRjlV0pYcBXxgXDfhlkOl55sLogvPEB/view?usp=sharing
7. Discovery Studio (Version 2022) https://discover.3ds.com/discovery-studio-visualizer-download
8. Marvin Sketch https://drive.google.com/file/d/18WN28mtb_ayVKFc09CgDaI5VBJVdESm9/view?usp=sharing

Pengaturan Path

1. Buka path, pada kolom search ketik path
2. Klik Enviromental Variabel
3. Klik Path Edit
4. Klik New, masukkan lokasi file atau folder pada path
5. Klik Ok sampai semua jendela tertutup (3 kali klik ok)
6. Yang harus dimasukaan dalam path ada 4 yaitu:
   1. C:\Program Files (x86)\MGLTools-1.5.7,
   2. C:\Program Files (x86)\ADFRsuite-1.0\bin and the location folder
   3. vina. exe
   4. vina_split.exe

Cara mengetahui active site dan binding sitenya

1. Baca artikel proteinnya
2. Menggunakan web Uniprot https://www.uniprot.org/
3. Menggunakan aplikasi Discovery Studio,
4. Menggunakan aplikasi server online seperti: ICM-PocketFinder, CASTp, Chimera, Qsite, Scfbio online server

Pemisahan ligand dan protein (Menggunakan Biovia Discovery Studio)

1. Pisahkan reseptor, buang air dan ligannya
2. Pisahkan ligand, buang protein, air

Preparasi Protein (Menggunakan Autodock Tools)

1. Dipisahkan air dan ligannya terlebih dahulu menggunakan Biovia Discovery Studio
2. Klik File Read Molecules cari protein dengan format .pdb
3. Dilakukan penambahan Hidrogen dengan Edit-Add Hidrogen-All
4. Edit tambahkan muatan gasteiger
5. Edit-Hidrogen Merge Non Polar
6. Grid-Macromolecules-Choose
7. save protein dengan nama 4ieh_protein.pdbqt

Preparasi Ligand (Menggunakan Autodock Tools)

1. Klik File Read Molecules cari ligand dengan format .pdb
2. Dilakukan penambahan Hidrogen dengan Edit-Add Hidrogen-All
3. Edit tambahkan muatan gasteiger
4. Edit-Hidrogen Merge Non Polar
5. Ligand-Input-choose
6. Pilih ligand.pdb
7. ligand-Toorsion tree-detect root
8. Klik Ligand-Torsion Tree-Choose Torsions, Klik Done
9. Klik Ligand-Torsion Tree-Set Number of Torsions Pilih fewest atom, selanjutnya klik Dismiss
10. Klik ligand-output-save as dengan nama 4ieh_ligand.pdbqt

Perintah di terminal untuk mengetahui Grid Box menggunakan Autogrid (Menggunakan Terminal)

1. Pastikan file prepare_gpf.py sudah ada difolder kerja, file ini bisa didownload menggunakan https://downgit.github.io/#/home dengan cara copy alamat ini https://github.com/purnawanpp/Docking-4ieh/blob/main/prepare_gpf.py ke website tersebut, lalu klik download
2. python.exe prepare_gpf.py -l 4ieh_ligand.pdbqt -r 4ieh_protein.pdbqt -y
3. autogrid4 -p 4ieh_protein.gpf -l 4ieh_protein.glg

Buat File GridBoxnya (Mengunakan Notepad), GridBox dibuat jika simulasi menggunakan AutoDock Vina

1. Buka file dengan 4ieh_protein.gpf
2. Catat npts 50 40 40 sebagai size x, y, z
3. Catat gridcenter -0.004 -0.187 0.078 sebagai center x, y, z
4. Buat file grid.txt didalamnya tertulis: center_x = -0.004 center_y = -0.187 center_z = 0.078 size_x = 50 size_y = 40 size_z = 40
5. Contoh file grid.txt dapat dilihat disini https://github.com/purnawanpp/Docking-4ieh/blob/main/grid.txt

OPSI 1-Prosedur Docking Autodock Vina (Menggunakan Terminal)

1. vina --receptor 4ieh_protein.pdbqt --ligand 4ieh_ligand.pdbqt --config grid.txt --exhaustiveness=8 --out 4ieh_ligand_vina_out.pdbqt > results.txt
2. vina_split --input 4ieh_ligand_vina_out.pdbqt

OPSI 2-Prosedur Docking Menggunakan AutoDock-GPU

1. Video tutorial ada disini: https://youtu.be/KotAUEJTDAY
2. Upload semua file hasil preparasi
3. Jalankan dan buka file script berikut di google colab: https://github.com/purnawanpp/Docking-4ieh/blob/main/Autodock_GPU.ipynb
4. Download file format .dlg dan buka menggunakan Notepad++, cari energi minimal dengan perintah run =

Perhitungan nilai RMSD (Menggunakan Biovia Discovery Studio)

1. Buka file 4ieh_ligand.pdbqt
2. Drag file 4ieh_ligand_vina_out_ligand_1.pdbqt
3. Klik File 4ieh_ligand.pdbqt,
4. Klik Structure-RMSD-Set Reference
5. Klik File 4ieh_ligand_vina_out_ligand_1.pdbqt
6. Klik Structure-RMSD-Heavy Atoms
7. Dibagian bawah nanti kelihatan nilai RMSDnya, nilai RMSD yang disarankan adalah <2

Perhitungan nilai RMSD (Menggunakan Terminal Linux dan OpenBabel ver 3.1)

1. Ketik diterminal : conda activate
2. Jalankan perintah diterminal: obrms -f 4ieh_ligand.pdbqt 4ieh_ligand_vina_out.pdbqt
3. Ubah file pdbqt menjadi pdb: obabel 4ieh_vina_out_ligand_1.pdbqt -O ligand1.pdb

Optimasi Geometri (Avogadro)

1. Buka Avogadro
2. Klik File-open-ligand/obat dengan format .mol2
3. Klik Extension-Molecular Mecahanics-Setup Force Field
4. Pilih setup Force-Field pilih MMFF94
5. Klik Extension-Pilih-Optimize Geometry
6. clik Save as, save format .mol2 file