Dataset for: Molecular Dynamics study of the Recognition of the Nucleic Acid Aptamer to ATP

Files with the initial aptamer structures (wt and three mutant forms) and their complexes with ATP after docking, used in the MD simulations, along with MD simulation trajectories and meta-eABF simulations, are included as tarballs (.tar.gz). Mutant structures were generated using PyMol, ATP docking performed using AutoDock Vina, and MD simulations based on NAMD software and Charmm36 and CGenFF force fields.

Funding by Swedish research council (VR), grant no. 2019-3684 (LAE).

Related Organizations

Beijing Institute of Technology
China (People's Republic of)
University of Gothenburg
Sweden

Keywords

ATP, MD simulations, Aptamer, pi-stacking, Recognition process

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