AMIGOS III Data

This entry includes all materials used to generate the figures and tables in the AMIGOS III publication (Shine et al., 2022). <br> AMIGOSIII-plugin-code.zip contains the code for the AMIGOS III PyMOL plugin, which can also be found at the following page: https://github.com/pylelab/AMIGOSIII. <br> Files beginning with "4en5" were used to generate Figure 1. This includes the 4en5.pdb file, which was used an an input for the AMIGOS III PyMOL plugin, and the following five output files, which were generated using the AMIGOS III NARama feature: 4en5_eta_theta_plot.png (an eta vs theta plot), 4en5_eta_theta_prime_plot.png (an eta' vs theta' plot), 4en5_nucleic_worm_plot.png (a 3D plot of nucleotide position, eta, and theta), 4en5_eta_theta.csv (a spreadsheet of eta and theta values), and 4en5_eta_theta_prime.csv (a spreadsheet of eta' and theta' values). <br> Files beginning with "7mk1-chainC" were used to generate Figure S2. This includes the 7mk1.pdb file, which was used an an input for the AMIGOS III PyMOL plugin, and the following five output files, which were generated using the AMIGOS III NARama feature: 7mk1-chainC_eta_theta_plot.png (an eta vs theta plot), 7mk1-chainC_eta_theta_prime_plot.png (an eta' vs theta' plot), 7mk1-chainC_nucleic_worm_plot.png (a 3D plot of nucleotide position, eta, and theta), 7mk1-chainC_eta_theta.csv (a spreadsheet of eta and theta values), and 7mk1-chainC_eta_theta_prime.csv (a spreadsheet of eta' and theta' values). <br> The AMIGOSIII-TableS1-FigureS1-ata.xlsx file contains the benchmark data underlying TableS1 and FigureS1, which compares the performance of the motif searching feature of AMIGOS III with the Perl program PRIMOS. <br>