All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions

<p>Topology files and frames extracted from the minimum of the free energy profile F(d_z) (or F(d_min) for single-stranded RNAs), within 2.5kBT. These files can be used to reproduce the hydrogen bond analyses in the manuscript.</p> <p>Scripts which were used to extract hydrogen bond information are available on <a href="https://github.com/salvatoredimarco/rna-membrane">https://github.com/salvatoredimarco/rna-membrane</a></p> <p><strong>Systems:</strong></p> <p>4xN: nucleosides</p> <p>4xN2: dinucleotides</p> <p>4xN3: trinucleotides</p> <p>4xN_OPC: nucleosides simulated with OPC water model. Energy threshold is here 1.0*kBT, because of weaker binding.</p> <p>1xGA, 1xGU, 1xGC, 1xCU</p> <p>1xGGC, 1xGCG</p> <p>1xquadruplex: G-quadruplex</p> <p>1xstrand: 19-mer RNA strand</p> <p>1xhairpin: 16-mer folded hairpin</p> <p>1x16mer_elong: 16-mer unfolded, restrained</p> <p>2x16mer_loose1/2: 16-mer unfolded, unrestrained</p>