The MM-PBSA algorithm was used to estimate the change of Gibbs free energy of substrate binding (∆Gb). From each trajectory, two ∆Gb estimates were received: total ∆Gb for the whole simulation and ∆Gbest estimated for the 5 nanoseconds simulation with the best geometry parameters of the bound substrate. These results were compared with MM-PBSA analysis of enzyme: substrate MD simulations of KstD1 from R. erythropolis , which were analysed according to the above protocol.