A Streamlit application that performs virtual screening with the GNINA molecular-docking software and conducts protein–ligand interaction analysis using PLIP.

1. 📝 Overview
2. 📦 Installation
   • GNINA Installation
3. 🏃 How to run
4. 📂 Input file formats & expected structure
5. 🔄 App workflows and usage
   • 🌀 Blind Docking
   • 🎯 Site-Specific Docking with Reference Ligand
   • 🧬 Residue Based Docking
6. 📚 Citation
7. 🤝 Acknowledgments

DOCK-IT is a comprehensive Streamlit-based application that facilitates virtual screening of compounds against protein targets using GNINA, an open-source molecular docking software. The application provides three distinct docking workflows with detailed interaction analysis. Everything is fully automated, eliminating manual steps and significantly reducing the time required for the entire process.

Key features include:

• Blind docking across entire protein structures

• Site-specific docking using reference ligands

• Residue-based docking with custom binding site definition

• SMILES to PDB conversion for ligand preparation

• Protein-ligand interaction analysis using PLIP

• Comprehensive results reporting with Excel formatting

• Fully automated workflows

Create new conda environment (Recommended):

From repository root, open terminal and run:

conda create -n dockit python=3.10

conda activate dockit

Install OpenBabel, swig, and PyMOL from conda-forge instead of pip:

conda install -c conda-forge openbabel swig pymol-open-source

• Alternatively, you can download PyMOL from the official website and add it to the system's PATH.

• Now, install other packages using pip:

pip install -r requirements.txt

Choose one of the following methods to install GNINA:

• Install GNINA from source code by following the instructions from the official repository:

  https://github.com/gnina/gnina

• Download GNINA Binary:

  Choose any of the following based on your hardware:

  If you have a GPU:

  wget https://github.com/gnina/gnina/releases/download/v1.3.2/gnina.1.3.2
  

  If you do not have a GPU:

  wget https://github.com/gnina/gnina/releases/download/v1.0.1/gnina
  

• Once you’ve downloaded the GNINA binary, rename it to gnina (removing the version number) and make the binary executable:

chmod +x gnina

• After making GNINA binary executable, note the full path to the binary file. For example:

  /home/gray_pc/apps/bin/gnina

• Open your shell configuration file, bashrc or zshrc (run in terminal):

nano ~/.bashrc

• Add the following line at the end (replace /home/gray_pc/apps/bin/gnina with your actual path):

export PATH="/home/gray_pc/apps/bin/gnina:$PATH"

• Save the file by:

  Ctrl+O → Writes the file.

  Prompt appears asking for the file name.

  Enter → Confirms the current file name and proceeds with saving.

  Ctrl+X → Closes the editor.

• Reload the shell:

source ~/.bashrc   # or source ~/.zshrc

Navigate to the directory containing the DOCK-IT app.py file and run in terminal:

streamlit run app.py

The application will open in your default web browser at http://localhost:8501

• Protein files must be in .pdb format, and all protein structures should be stored in a single directory.

• DOCK-IT supports ligand input in two ways:

  a. .pdb format ligand files stored in a single directory.

  b. A .csv file containing SMILES strings along with molecule names or IDs.

• The application will automatically convert SMILES to 3D structures in .pdb format

• Reference Ligand Files (for site-specific docking):

  The required format is .pdb files of protein–ligand complexes, containing protein structures with their bound reference ligands.

  The application will automatically extract the ligand coordinates from these files to define the binding site.

DOCK-IT provides three distinct docking workflows:

Screen ligands against the entire protein surface to identify potential binding sites.

Workflow:

• Input protein PDB files directory

• Input ligands (either as PDB files directory or SMILES CSV file)

• Set docking parameters (scoring function, exhaustiveness, etc.)

• Run screening

• Review results with detailed interaction reports

Focus docking on a specific binding site using a known reference ligand.

Workflow:

• Input protein PDB files directory

• Input reference ligand complexes directory

• Input screening ligands (PDB files directory or SMILES CSV file)

• The application automatically maps proteins to reference ligands based on sequence similarity

• Set docking parameters including binding box padding around reference ligand

• Run targeted screening

• Review results with detailed interaction reports

Define a custom binding site by specifying specific protein residues.

Workflow:

• Input protein PDB files directory

• Input screening ligands (PDB files directory or SMILES CSV file)

• Specify residue positions for each protein using format:

  Individual residues: 45+67+23

  Residue ranges: 79-100 or 20-27+45+63-76

• Adjust bounding box size with interactive 3D visualization

• Set docking parameters

• Run targeted screening

• Review results with detailed interaction reports

All workflows include:

• Automatic pose splitting and complex creation

• Protein-ligand interaction analysis using PLIP

• Formatted Excel reports

• Per-protein result organization

If you use DOCK-IT in your research, please cite:

DOCK-IT. GitHub: https://github.com/usman4373/DOCK-IT

• GNINA development team for the excellent docking software
• Streamlit team for the powerful web application framework
• All open-source libraries that make this project possible