Rigidity Theory-Based Approximation of Vibrational Entropy Changes upon Binding to Biomolecules

We introduce a computationally efficient approximation of vibrational entropy changes (ΔSvib) upon binding to biomolecules based on rigidity theory. From constraint network representations of the binding partners, ΔSvib is estimated from changes in the number of low frequency (“spongy”) modes with respect to changes in the networks’ coordination number. Compared to ΔSvib computed by normal-mode analysis (NMA), our approach yields significant and good to fair correlations for data sets of protein–protein and protein–ligand complexes. Our approach could be a valuable alternative to NMA-based ΔSvib computation in end-point (free) energy methods.