I’m excited to share my latest computational tool for the molecular modeling community: Protonation Optimizer - a (SemiEmpirical) quantum mechanics-based solution for determining optimal amino acid protonation states in protein structures!

🔬 Why it matters: Accurate protonation states are critical for reliable molecular dynamics (MD) simulations, yet they’re often overlooked. Incorrect assignments can lead to artifacts or misleading results, particularly with histidine residues that can exist in multiple tautomeric forms for the same pH conditions.

⚡ Key features:

Integrates PropKa3 for pKa predictions and initial state assignments. Employs xTB semi-empirical quantum chemistry calculations to determine energetically favorable protonation states. Handles both HID (δ-protonated) and HIE (ε-protonated) histidine tautomers with QM accuracy. Provides detailed energy reports and automatically generates optimized PDB files.

🔗 Check it out: Protonation-Optimizer

Feel free to use it and let me know how it went!

Protonation State Optimizer

A quantum mechanics-based tool for determining optimal aminoacidic protonation states (focusing on Histidines) in protein structures for molecular dynamics simulations.

Description

This tool analyzes protein structures and determines the energetically favorable protonation state for each histidine residue using the xTB semi-empirical quantum chemistry method (HID/HIE). It accurately handles the two neutral tautomeric forms of histidine by:

1. Checks pKa using the PropKa3 tool. It determines HIP protonation based on pKa
2. Extracting the local environment around each histidine residue
3. Generating both HID (delta-protonated) and HIE (epsilon-protonated) tautomers
4. Special handling of charged residues (ASP, GLU, LYS, ARG) with proper proton positioning
5. Running quantum mechanical energy calculations on each tautomer
6. Comparing energies to determine the optimal protonation state

This tool is particularly useful for preparing protein structures for molecular dynamics simulations where histidine protonation can significantly impact results.

Dependencies

Python Packages

• NumPy
• Pandas
• MDTraj
• BioPython (Bio.PDB)
• Tabulate

External Software

• Open Babel (for hydrogen placement)
• xTB (for quantum mechanical calculations)
• PropKa3

Installation

1. Install the required Python packages:

2. Install Open Babel:

3. Install xTB:

4. Install PropKa3

5. Clone the repository:

   git clone https://github.com/miqueleg/protonation-optimizer
   

Usage

Basic usage:

python protonation_optimizer.py input.pdb output.pdb

With custom environment cutoff (default is 5.0 Å):

python protonation_optimizer.py input.pdb output.pdb --cutoff 6.0

Changing Optimization level and Solvent (default loose and ether) :

python protonation_optimizer.py input.pdb output.pdb --xtbopt crude --solvent water

Using Single Point calculations instead of Optimization [Faster but less precise] (default opt) :

python protonation_optimizer.py input.pdb output.pdb --mode SP

This will:

1. Run PropKa3 and determine initial protonations
2. Find all histidine residues in protein.pdb
3. For each histidine, extract a 5.0 Å environment
4. Create both HID and HIE tautomers with proper hydrogen placement
5. Run xTB optimization or single point calculations on each tautomer
6. Determine the optimal protonation state based on energy
7. Generate a detailed report table of the analysis

Output Files

The tool generates several outputs:

• An optimized PDB file with the computed protonation states of the AminoAcids in your protein
• A CSV file with energy results for each histidine
• A detailed text report of the analysis
• xTB log files for each calculation in an xtb_logs directory

Special Features

• Charged Residue Handling: It handles ASP, GLU, LYS, and ARG by pKa/pH comparison using PropKa3
• Constraint-based Optimization: Allows hydrogen atoms to relax during energy calculations while keeping heavy atoms fixed

Limitations

• Only handles the two neutral tautomers via QM (HID and HIE), not the protonated form (HIP). The latest is only determined via pKa calculation
• Processes each histidine independently; for histidines in close proximity, results may not capture cooperative effects (yet)

Citing This Software

If you use this tool in your research, please cite it as:

Estévez-Gay, M. (2025). Protonation State Optimizer.
GitHub repository: https://github.com/miqueleg/protonation-optimizer