A comprehensive protein reaction coordinate optimization framework
Project description
cg_r_pathway
cg_r_pathway is a comprehensive protein reaction coordinate optimization framework that integrates:
- Physics-based Modeling: Residue-specific parameters (mass, charge, ε, σ, hydrophobicity), bonds, angles, nonbonded interactions.
- Advanced Optimization: Global path optimization using Adaptive PSO+SA and local refinement using Double-Nested Simulated Annealing (DSA-ASA).
- Self-Learning ML Model: A placeholder neural network force field for continuous improvement.
- Coarse-Graining and Backmapping: Converting full-atom PDB structures to a coarse-grained model and reconstructing all-atom models via rigid-body transformation.
- Advanced Visualization: Reaction coordinate (RMSD vs Energy) plots and 3D path visualization.
Installation
Clone the repository and install with pip:
pip install .
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