Explanation
Explanation pages help you understand why PolyzyMD works the way it does, how to interpret outputs, and what assumptions or tradeoffs matter.
Tip
Looking for step-by-step instructions? Go to How-To Guides. Need to look up a setting or option? Go to Reference.
How the analysis pipeline, chain conventions, and plugin architecture fit together.
Replication, convergence, multiple testing, and per-plugin best practices.
Interpretation guidance for experimental analysis workflows.
Concepts and Design
Interpretation and Best Practices
Experimental Analysis Concepts
These workflows remain available in PolyzyMD, but their interpretation is still evolving and they should be treated as experimental. See also the how-to guides for Binding Preference Analysis, Binding Free Energy Analysis, Polymer Affinity Score Analysis, and Exposure Dynamics Analysis.