Dataset related to the article "A Minimal Mutation Trajectory Separates Inverting and Retaining Mechanisms on the Same Sialidase Structural Scaffold"

This dataset contains files related to the article "Two mutations alter the inverting mechanism of a specific sialidase to retaining" by Michael Jakob Pichler, Marina Corbella, Sebastian Meier, Tine Sofie Neilsen, Sanchari Banerjee, Jens Preben Morth, Carme Rovira and Maher Abou Hachem. Description of the files: Simulation data: - classical_md_simulations: includes the inputs, topologies, starting coordinates and starting pdb structures of the classical MD simulation of AmGH181 unliganded and wild-type and H349A/Q350Y in complex with sialyl T-antigen, as well as the restart files of each of the three replicates every 100 ns of simulation. - qmmm_simulations: includes the inputs for equilibration and metadynamics, topologies and the starting structures extracted from the classical MD simulations for the Inverting (wild-type liganded) and Retaining (H349A/Q350Y) reaction mechanisms, as well as the restart files every 10 ps of simulation and HILLS files. Relevant structures for the reactant states (RS.pdb), transition states (TS.pdb), product states (PS.pdb) and relaxed product states (PS_relax.pdb) along each path, are included in thei corresponding directories.