Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA

Data deposition for "Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA" published in Nucleic Acids Research. Data includes custom paramaterized nucleobase residues for use in AMBER molecular dyanmics simulations. Initial structures and setup code along with starting structures for generation of simulations in AMBER (pmemd.cuda). A in-house "MD-Generator" script to create nessessary files with our select simulation settings. Lastly, also included are CPPTRAJ analysis commands and scripts with visualizion scripts for use in Pymol 2.5 and above.