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About PRISM

PRISM (Protein Receptor Interaction Simulation Modeler) is a comprehensive Python toolkit for building and analyzing protein-ligand molecular dynamics systems.

Mission

PRISM's mission is to make high-quality molecular dynamics simulations accessible to researchers by automating the complex workflow of system preparation, simulation setup, and trajectory analysis.

History

PRISM was developed at the Institute of Quantitative Biology, Zhejiang University, starting in 2023 to address the need for:

  • Automation: Eliminate manual, error-prone system building steps
  • Flexibility: Support multiple force field options
  • Reproducibility: Consistent, documented workflows
  • Accessibility: Lower barriers for non-experts

Key Features

System Building

  • Automated protein-ligand system construction
  • 8+ ligand force field options (GAFF, GAFF2, OpenFF, OPLS-AA, CGenFF, MMFF, MATCH, Hybrid)
  • Multiple protein force fields (AMBER, CHARMM, OPLS)
  • Intelligent protein preparation with metal ion handling
  • One-command GROMACS integration

Analysis

  • Comprehensive trajectory analysis (RMSD, RMSF, contacts, H-bonds)
  • Interactive HTML visualizations
  • Automated plotting and reporting
  • Publication-quality figures

Advanced Calculations

  • PMF/Umbrella sampling for binding free energies
  • MM/PBSA calculations
  • Batch processing for high-throughput screening
  • Parallel execution support

Design Philosophy

  1. Simple for Simple Tasks: Common workflows should be one command
  2. Flexible for Complex Tasks: Full control when needed
  3. Reproducible: All settings documented and version controlled
  4. Well-Documented: Clear examples and comprehensive docs
  5. Open Source: Free and community-driven

Technology Stack

  • Language: Python 3.8-3.11
  • MD Engine: GROMACS 2024.3+
  • Force Fields: AmberTools, OpenFF, LigParGen, ParamChem
  • Analysis: MDTraj, NumPy, SciPy, Matplotlib
  • Visualization: RDKit, Plotly, custom HTML generators

Use Cases

Drug Discovery

  • Virtual screening of compound libraries
  • Binding affinity prediction
  • Force field validation

Structural Biology

  • Protein-ligand binding mechanisms
  • Conformational changes
  • Allosteric effects

Method Development

  • Force field comparison and benchmarking
  • Protocol optimization
  • Algorithm testing

Community

PRISM is developed and maintained by researchers, for researchers. We welcome:

  • Bug Reports: Help us improve reliability
  • Feature Requests: Tell us what you need
  • Contributions: Code, docs, examples
  • Feedback: What works, what doesn't

Getting Involved

  • GitHub: github.com/AIB001/PRISM
  • Discussions: Share ideas and get help
  • Issues: Report bugs and request features
  • Email: Contact the development team

Citing PRISM

If you use PRISM in your research, please cite:

@software{prism2024,
  author = {Shi, Zhaoqi},
  title = {PRISM: Protein Receptor Interaction Simulation Modeler},
  year = {2024},
  version = {1.2.0},
  institution = {Institute of Quantitative Biology, Zhejiang University},
  url = {https://github.com/AIB001/PRISM}
}

Acknowledgments

PRISM development has been supported by: - Institute of Quantitative Biology, Zhejiang University - Open source community contributions - Feedback from users worldwide

License

PRISM is released under the MIT License, allowing free use in academic and commercial settings. See License for details.

Developed at: Institute of Quantitative Biology Zhejiang University

Principal Developer:
Zhaoqi Shi

Contact:
zshi268@wisc.edu