Figure 1.
The native structure of the GA module of an albumin binding domain.
Three representations of the structure are shown. The left panel shows the backbone of the native fold as a ribbon, which highlights the helical nature of the secondary structure. The center panel shows the AA structure, which is used to build the KT G model (right panel).
Figure 2.
The fraction of native contacts are plotted as a function of time. By inspecting the histogram at the right, we observe that this trajectory was simulated below , as the protein is folded for 62% of the simulation.
Figure 3.
Each point on the plot represents calculated from a full trajectory.
occurs when
, and the curvature of the plot is related to
.
Table 1.
1PRB thermochemistry.
Figure 4.
The workflow of the KT G model lesson.
Blue boxes represent the steps described in the text. Yellow boxes show the inputs and outputs of each step. Note that the CHARMM protein structure file is only built when a calculation is performed (minimization, in this case). Q is the fraction of native contacts as defined in the text.