pmx: Automated protein structure and topology generation for alchemical perturbations.

Abstract excerpt

Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies...

Topics

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• Amino Acids
• Automation
• Gene Library
• Molecular Dynamics Simulation
• Protein Stability