Data and analysis scripts for: Domain misannotation in BAG3: AlphaFold3 and molecular dynamics show the second WW domain is disordered

This dataset contains the AlphaFold3 structural models, molecular dynamics analysis outputs, and analysis scripts supporting the manuscript "Domain misannotation in BAG3: AlphaFold3 and molecular dynamics show the second WW domain is disordered," submitted to the Journal of Molecular Graphics and Modelling. Contents include: AlphaFold3 model files (model3.cif, model_4_processed.pdb (model3)); the murine NMR reference structure used for validation (1UK5.pdb) and its residue-mapping verification script; per-residue pLDDT and PAE analysis scripts (F1, F2); contact persistence analysis (A1, A1b); PAE-versus-flexibility, heterogeneity, disorder-prediction, and dimension analyses (A2–A5); a consensus summary table script (A6); RMSIP subspace convergence analysis (F11); burn-in diagnostics (F15); secondary-structure cross-validation via DSSP and P-SEA (F16); an independent disorder predictor cross-check (F17); BAG-domain conformational clustering (F14 and replot script); best-frame selection and structural rendering scripts; and the summary figures generated from these analyses (pLDDT profile, PCA loadings, secondary-structure fraction, per-replica PCA projections, and the dynamic cross-correlation map). Raw molecular dynamics trajectory files (three replicate 100 ns simulations per system) are not included due to file size and are available from the corresponding author upon reasonable request.