Table 1.

Kinetic parameters of the CDK2–ligand-binding process determined by conventional and hypersound-perturbed MD simulations. The values are presented as the mean ± SD.

	Association rate constant kon (M−1 s−1)	Activation energy E (kcal mol−1)a	Diffusion constant D (×10−5 cm2 s−1)	Steric factor log(ρ)	Frequency factor log(A (M−1 s−1))	Effective temperature T (K)
CS3 (conventional MD)	3.35 × 105b	3.9 ± 1.8	0.17 ± 0.05	−0.76	8.35 ± 0.13	298
CS3 (hypersound-perturbed MD)c	3.68 × 106	3.9 ± 1.8	0.61 ± 0.16	−0.76	8.91 ± 0.12	362
CS242 (conventional MD)	3.21 × 104b	6.7 ± 2.4	0.19 ± 0.07	0.20	9.36 ± 0.17	298
CS242 (hypersound-perturbed MD)c	1.92 × 106	6.7 ± 2.4	0.30 ± 0.10	0.20	9.56 ± 0.15	445

^aThe E parameter was estimated from hypersound-perturbed MD simulations with N = 50 steps, v_max = 400 m/s, and T_int = 2400 N, assuming that the activation energy is not affected by the hypersound irradiation.

^bExperimentally determined k_on values retrieved from the Community Structure-Activity Resource (CSAR) database¹⁶.

^cHypersound shock waves with the same parameters as above were used to determine the k_on, D, A, and T parameters, which vary depending on the hypersound parameters (Supplementary Table 3).