Examining asymmetric pairwise pre-reaction and transition states in enzymatic catalysis by molecular dynamics simulation and quantum mechanics/molecular mechanics calculation.

ABSTRACT: Here, we present a protocol to examine asymmetric pairwise pre-reaction and transition states in enzymatic catalysis. We describe steps to set up the calculated systems, run umbrella sampling molecular dynamics simulation, and conduct quantum mechanics/molecular mechanics calculations. We also provide analytical scripts to yield potential of mean force of pre-reaction states and reaction barriers. This protocol can generate quantum-mechanistic data for constructing pre-reaction state/transition state machine learning models. For complete details on the use and execution of this protocol, please refer to Luo et al. (2022).¹.

SUBMITTER: Luo S 

PROVIDER: S-EPMC10172999 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature