Figure 11.

(A) The RMSD plot for the reference inhibitor SRI-9662 complexed with hDHFR (PDB: 1KMV) over a 100 ns simulation time; (B) Stability of the hDHFR secondary structure over 100 ns of MD simulation when complexed with SRI-9662. Protein secondary structure elements (SSE) like alpha-helices (orange color) and beta-strands (light blue color) were monitored during the simulation. The upper plot reported SSE distribution by residue index across the protein structure, and the plot at the bottom monitored each residue and its SSE assignment over the simulation time.