Figure 3
From: Stereochemical errors and their implications for molecular dynamics simulations
Impact of stereochemical errors on the structure of an α -helix. Impact of stereochemical errors on the structure of an α-helix. The figure shows the starting conformations, the conformations after 32 ns of equilibrium simulation, as well as the secondary structure content throughout the simulation for (A) a stereochemically correct helix, (B) a helix with a D-Gln8, and (C) a helix with a cis peptide Gln8-Ala9. The axis on the left shows residue numbers and the red dashed line indicates the position of the introduced stereochemical errors. The colors in the bottom panels represent secondary structure content: helix (pink), turn (cyan) and coil (white).