E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands

Abstract

We present E2EDNA 2.0: End-2-End DNA 2.0, a Python simulation pipeline that offers a unified and automated solution to computational modeling of DNA aptamers with molecular ligands. It is broadly aimed at researchers developing therapeutics and sensors based on DNA aptamers who require detailed atomistic information on the behavior of aptamers and ligands in realistic media. Similar to its predecessor E2EDNA (Kilgour et al., 2021), E2EDNA 2.0 predicts DNA aptamers’ secondary and tertiary structures, and if a ligand is present, the configuration of the solvated aptamer-ligand complex.