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FleXgeo2 Wiki

FleXgeo2 is a refactor of FleXgeo built around Melodia_py. It computes protein backbone differential-geometry descriptors from PDB files and helps researchers study ensemble-aware curvature, torsion, local flexibility, reference-state differences, and conformational clusters.

Pages

• Installation
• Quickstart Analysis
• Command Line Guide
• Python Library Guide
• Understanding Outputs
• dmax Flexibility Metric
• Reference-State Comparison
• Clustering Conformations
• Notebook Tutorials
• Citation

When to use FleXgeo2

Use FleXgeo2 when you want to compare local protein backbone geometry across a PDB ensemble without relying on structural superposition alone. The main workflows are:

• finding residues with large curvature/torsion variation across models
• summarizing ensemble flexibility with per-residue dmax
• comparing every model to a chosen reference state
• clustering conformations residue-by-residue or across a residue window
• exporting reproducible CSV tables and plots for downstream analysis

For the fastest path through the software, start with Installation and Quickstart Analysis. For deeper analysis examples, see Notebook Tutorials.

Used the April 2026 preview tagged v2.0.0? The output layout, some options and model numbering have changed since; the changelog lists what changed and where each file went.