Explanation

Explanation pages help you understand why PolyzyMD works the way it does, how to interpret outputs, and what assumptions or tradeoffs matter.

Concepts and Design

• Architecture

• Residue Assignment and Chain Conventions

• Colored Logging

Analysis Interpretation and Best Practices

• Statistical Best Practices for Analysis

• RMSF Best Practices

• RMSF Reference Selection

• RMSF Verification

• Catalytic Triad Best Practices

Experimental Analysis Concepts

These workflows remain available in PolyzyMD, but their interpretation is still evolving and they should be treated as experimental:

• Binding Preference

• Binding Free Energy

• Polymer Affinity

• Exposure Dynamics