Structure-Guided Engineering of a Multifunctional Glycosidase for Exclusive High-Yield Production of Ginsenoside F1 from Panax notoginseng - Simulation files

This dataset contains the molecular docking and molecular dynamics (MD) simulation data generated for the study entitled "Structure-Guided Engineering of a Multifunctional Glycosidase for Exclusive High-Yield Production of Ginsenoside F1 from Panax notoginseng". The simulations investigate the binding dynamics and conformational changes of the wild-type (WT) β-glucosidase BgDU (glycoside hydrolase family 3, GH3) and its DUase mutant in complex with substrates NG-R1 and G-Rg1 over 50-nanosecond (ns) production runs. Four independent simulations were performed: 1.WT enzyme + NG-R1 substrate 2.WT enzyme + G-Rg1 substrate 3.DUase mutant + NG-R1 substrate 4.DUase mutant + G-Rg1 substrate The data is organized into four main folders for clarity: 1.Docking Structure: Contains coordinate files in PDB format derived from computational modeling and database sources for molecular docking. Specifically, the wild-type β-glucosidase BgDU and DUase mutant structures were predicted using AlphaFold3; the NG-R1 and G-Rg1 substrate structures were extracted from the PubChem Compound Database; and the docked complexes were generated by molecular docking between these protein and ligand structures. These files serve as the starting points for subsequent molecular dynamics simulations. 2.MD Structure: Contains coordinate files in PDB format sampled at key time points during the 50 ns production runs. Files represent snapshots at 0 ns, 10 ns, 20 ns, 30 ns, 40 ns, and 50 ns for each simulated system. 3.Topology: Contains topology files (*.itp) defining the force field parameters specific to the substrates NG-R1 and G-Rg1. This includes RESP2 atomic charges derived using Multiwfn and GROMACS-compatible ITP files generated by sobtop that integrate RESP2 charges. 4.MDP: Contains all molecular dynamics parameter (*.mdp) files used to control the simulation protocol within GROMACS.