Figure 3.

Combined workflow for comparing existing experimental structures and simulations. (a) The workflow contains two main parts: experimental structure ensemble analysis (green shading, left) and ClustENM simulations (blue shading, right). The experimental structures are aligned into an ensemble (red box) and analysed by PCA (central blue box) and RMSD clustering (left orange box). Some representative clusters are also used for NMA (3 blue boxes outside green shading) to confirm the best structure for simulations via comparison of NMs and PCs (following green boxes). Some atomic structure tools (yellow) were also used including as a first step to prepare the structure for simulations. Coloured arrows connect to other panels showing their outputs. (b) A combined landscape is shown projecting the experimental ensemble in orange and the simulated one in blue in the space of the first two principal components from the experimental ensemble (axis values are in units of RMSD in Å). The main conformations are labelled, including the simulation starting structure (PDB: 7KEC). (c) An overlap matrix is shown comparing the first five non-zero ANM normal modes of the 1-up, 1-I structure (PDB: 7KEC) to the first five principal components of the ensemble with low overlaps in blue and high overlaps in green, orange and red.