PMX

PMX generates hybrid protein structures and topologies for alchemical molecular dynamics to calculate free energy changes associated with amino acid mutations.

Key Features:

• Hybrid Structure Generation: Creates hybrid protein structures that represent end states of amino acid mutations for alchemical transformations.
• Topology Support: Generates topologies in five contemporary molecular mechanics force fields to ensure compatibility with multiple simulation parameterizations.
• Mutation Scanning: Performs comprehensive mutation scans using a user-defined amino acid to explore variant effects on proteins.
• Gromacs Compatibility: Produces outputs that are directly compatible with the Gromacs molecular dynamics engine.
• Database Access: Provides a database of input files and precalculated free energy differences for tripeptides that approximate disordered protein states.

Scientific Applications:

• Alanine Scans: Enables systematic alanine scanning to evaluate residue contributions to protein stability.
• Thermodynamic Stability Studies: Supports investigation of protein thermodynamic stability, including case studies such as the Trp cage mini-protein.

Methodology:

Generates hybrid structures and topologies for alchemical molecular dynamics, supports topology generation in five molecular mechanics force fields, enables mutation scanning, produces Gromacs-compatible output, and provides precalculated tripeptide free energy differences.