Molecular Graphics and Visualization

The above figure shows barcharts representing the dominant secondary structure of a protein calculated from the secondary structure time series for a given molecular dynamics simulation. It shows secondary structure elements that are present for at least 90% of the simulation time for the various simulation runs. The dominant secondary structure analysis makes secondary structure comparisons between different simulations easier. This representation was introduced in the recently published computational work on OmpT where we describe molecular dynamics simulations and docking of several tetra-peptides [[Baaden 2004]] and has since been used in a number of computational studies of membrane proteins. The graphs were produced via a script run over the production data of all simulations. The script was specifically developed for this purpose and uses SDF, GNU make, Gromacs, dssp, perl, imagemagick and xmgrace.