Structural variations of plexin-B1 models b1.1, b1.2 and b1.3 (panels a,b,c respectively) in MD simulations (TM + flanking residue simulations).

<p>RMSD (top), crossing (middle) and helix rotation angles (bottom panel), calculated as in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.ref009" target="_blank">9</a>]. Rotation angles for helix A in black, helix B in red. The data (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#sec020" target="_blank">methods</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.t002" target="_blank">Table 2</a>) suggest that 1 μs MD simulations are typically sufficient for the refinement. However, slower reversible changes are seen in simulation B1.1 which was continued to 2 μs. Standard deviations of RMSD and geometric parameters over the last 250 ns of the simulations were used to confirm equilibration.