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pdb2reaction is a Python CLI toolkit for analyzing reaction mechanisms in enzyme complexes and small molecules with machine-learning interatomic potentials (MLIPs), starting from PDB/mmCIF/XYZ/GJF str
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End-to-end Reaction-Path Modeling from PDB Structures Using Machine-Learning Interatomic Potentials
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pdb2reaction: End-to-End Reaction-Path Elucidation from PDB Structures Using Machine-Learning Interatomic Potentials
pdb2reaction is a Python CLI toolkit for analyzing reaction mechanisms in enzyme complexes and small molecules with machine-learning interatomic potentials (MLIPs), starting from PDB/mmCIF/XYZ/GJF structures.
You can test a reaction mechanism in a single command like:
Starting from the reactant (R) and product (P) structures, the command above runs:
Active-site cluster model setup → Minimum energy path (MEP) search → TS optimization → IRC → ThermochemistryRead the full README ↗The full README is unavailable right now. Read it at the original link. The saved excerpt is shown below.
pdb2reaction: End-to-End Reaction-Path Elucidation from PDB Structures Using Machine-Learning Interatomic Potentials
pdb2reaction is a Python CLI toolkit for analyzing reaction mechanisms in enzyme complexes and small molecules with machine-learning interatomic potentials (MLIPs), starting from PDB/mmCIF/XYZ/GJF structures.
You can test a reaction mechanism in a single command like:
Starting from the reactant (R) and product (P) structures, the command above runs:
Active-site cluster model setup → Minimum energy path (MEP) search → TS optimization → IRC → ThermochemistryRead the full README ↗