Supplementary information.

Fig A. Correlation between miR-125a maturation efficiency and Dynamical Signature distance to WT for both ENCoM and MD simulations. Fig B. Cut-ANM and PD-ANM parameter sweep for the B-factors benchmark. Fig C. Performance of multiple linear regression on an 80–20 train-test split. Fig D. Size distributions of the sequence clusters from the 3 benchmarks. Fig E. Number of nontrivial normal modes at 5% for the overlap and NMR benchmarks. Fig F. Simulation of predictive R-squared from combinations of MC-Fold enthalpy with random noise. Fig G. Computational cost of the ENMs on the Thermus thermophilus 30S ribosomal subunit and on miR-125a. Table H. Atom type assignation of the four standard nucleotides. Table I. PDB codes of the structures used for the three benchmarks. Table J. Performance on individual structures for the B-factors correlation benchmark. Table K. Performance on individual pairs of conformations for the X-ray conformational change benchmark. Table L. Performance on individual NMR ensembles for the ensemble variance benchmark. Table M. MD trajectories of miR-125a variants. Table N. ENCoM interaction strength for different base pairs.

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