Interpretation
PyMACS translates raw trajectories into plots, CSV tables, networks, and figurebooks. The goal is not just to produce files, but to make the simulation interpretable.
| Output | What it helps answer |
|---|---|
| Protein_RMSD.png | Did the protein drift or settle? |
| FullComplex_RMSD.png | Did the whole simulated assembly remain coherent? |
| RMSF plots | Which residues, chains, or ligand atoms were flexible? |
| Radius_of_Gyration_Overlay.png | Did the system compact, expand, or breathe? |
| DSSP_Heatmap.png | Did secondary structure persist or change? |
| Output | Meaning |
|---|---|
| AllContacts_Framewise.csv | Frame-by-frame contact table before filtering. |
| FilteredContacts_Framewise.csv | Contacts passing persistence or cutoff rules. |
| InteractionTypes_Framewise.csv | Interaction classifications over time. |
| InteractionTypes_Summary.csv | Residue-level interaction summary. |
| interaction_heatmap_normalized.png | Heatmap of persistent residue/interaction behavior. |
| binding_importance_ranking.png | Ranked residues for interpretation. |
Contact analysis is based on geometric cutoffs and residue chemistry. It is evidence of proximity, persistence, and interaction type; it is not a direct binding free energy calculation.
The figurebook scripts collect useful plots into MD_ANALYSIS_FIGUREBOOK.pdf or PROTAC_MD_ANALYSIS_FIGUREBOOK.pdf so users can review results without hunting through the output tree.