Supplementary Material for Genome-wide modulation of alternative splicing by a predicted alpha helix in U2AF2

Supplementary Material: AlphaFold-predicted protein structure coordinates, PyMOL scripts, and GROMACS MD simulation files AlphaFold-predicted protein structure coordinates: UAF-1 (C. elegans ortholog of U2AF2) and U2AF2 (human), as well as their heterodimeric complexes with UAF-2 (C. elegans ortholog of U2AF1) or U2AF1 (human). For each target, we provide mmCIF coordinate files for the five ranked models, per-residue confidence scores (pLDDT) in the summary_confidences JSON files, full prediction metadata (including PAE matrices and model details) in the full_data JSON files, the original job request JSON, and the terms of use. PyMOL scripts: U2AF65 RNAH motif conformation analysis using PyMOL 2.5 (open-source version, https://github.com/schrodinger/pymol-open-source). The parameters of the RNAH motif, including the helical tilt angle, local twist, and root mean square deviation (RMSD), as well as the generation of the helical axis centerline, were calculated using custom Python scripts integrated with PyMOL. GROMACS MD simulation files: including the binary input run file (extracted_traj.tpr) and the compressed trajectory (extracted_traj.xtc), together with hydrogen‑bond analysis outputs and the associated scripts used to generate them.