Fig 1.
Workflow of the ProProtein platform.
Fig 2.
A heuristic for identification of high-fluctuation 3D motifs of interest.
Fig 3.
Example MD simulation results.
Panel A shows the human lymphotactin protein model with an unfolded C-terminal fragment, representing the starting structure of the MD production run. Panel B presents the formation of a loop in the C-terminal fragment at 5 ns (high-fluctuation 3D motifs are depicted in red color). Panel C shows the HB interactions in the folded C-terminal fragment at 10 ns. Panel D shows proximal residues of the C-terminal fragment at 15 ns, where an altered hydrogen bonding network stabilizes the bent C-terminal conformation.
Fig 4.
Example MD simulation results.
Panels A and B show the human ubiquitin protein model at the five ns MD production run. Panels C and D show the ubiquitin model at the 15 ns of the simulation run. High-fluctuation 3D motifs are shown in red color (panel A).