PRISM¶

Protein Receptor Interaction Simulation Modeler

A comprehensive toolkit for building and analyzing protein-ligand MD systems

Overview¶

PRISM is a Python framework for building protein-ligand systems and analyzing MD trajectories, developed at the Institute of Quantitative Biology, Zhejiang University. It automates the complex workflow of preparing molecular dynamics simulations with multiple force field options and provides comprehensive analysis tools.

Quick Start¶

Command LinePython APIInstallation

# GAFF (default)
prism protein.pdb ligand.mol2 -o my_system

# OpenFF
prism protein.pdb ligand.sdf -o my_system --ligand-forcefield openff

# Multiple ligands
prism -pf protein.pdb -lf lig1.mol2 -lf lig2.mol2 -o my_system

import prism

# Build system with GAFF force field (default)
system = prism.system("protein.pdb", "ligand.mol2", output_dir="my_system")
system.build()

git clone https://github.com/AIB001/PRISM.git
cd PRISM
pip install -e .

Key Features¶

Automated System Building¶

One-command setup for protein-ligand MD systems with automated protein cleaning, ligand parameterization, solvation, and neutralization.

Multiple Force Fields¶

Support for 8+ ligand force fields: GAFF, GAFF2, OpenFF, CGenFF, OPLS-AA, MMFF, MATCH, and hybrid approaches.

Trajectory Analysis¶

Comprehensive analysis tools including RMSD/RMSF, contacts, hydrogen bonds, clustering, SASA, and dihedral angles.

Interactive Visualization¶

Generate interactive HTML visualizations of protein-ligand contacts with customizable 2D/3D views.

GROMACS Integration¶

Native GROMACS workflow with auto-generated MDP files for EM, NVT, NPT, and production MD.

Advanced Calculations¶

Built-in support for PMF (umbrella sampling/WHAM) and MM/PBSA binding energy calculations.

Core Modules¶

Module	Description
Builder	Automated system construction: force field generation, protein preparation, solvation, topology output
Simulation	Complete EM → NVT → NPT → Production pipeline with auto-generated run scripts and GPU support
Analysis	RMSD, RMSF, contacts, H-bonds, SASA, clustering, PCA, interactive HTML reports
PMF	Steered MD setup, automated umbrella sampling window generation, WHAM analysis
MM/PBSA	Single-frame and trajectory binding energy with electrostatic, vdW, solvation decomposition

System Requirements¶

Required

Python 3.8 - 3.11 (3.10 recommended)
GROMACS 2024.3+ (CUDA support recommended)
PDBFixer, NumPy, SciPy

Force Field Specific

GAFF/GAFF2: AmberTools, ACPYPE
OpenFF: OpenFF Toolkit, OpenFF Interchange
CGenFF: Downloaded parameters from ParamChem
OPLS-AA: Internet connection (LigParGen)

Documentation¶

Getting Started -- Installation and basic usage
User Guide -- Comprehensive feature documentation
Tutorials -- Step-by-step guides and examples
API Reference -- Complete API documentation
Examples -- Real-world use cases and scripts

Contributing¶

git clone https://github.com/your-username/PRISM.git
cd PRISM && pip install -e .[dev]
pytest tests/

For questions or suggestions, open an issue on GitHub.

Citation¶

@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}
}

Institute of Quantitative Biology | Zhejiang University | Author: Zhaoqi Shi