Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

Figure 5

Representative structures of chignolin obtained by the SAAP-MC simulation at 300 K in water. The obtained 20,000 structures were analyzed by a structural clustering algorithm using the 𝑘-means method. Structures (A), (B), and (C) were obtained based on the main-chain RMSD. Structure (A′) was obtained based on the all-atom RMSD. Distances of the hydrogen bonds and the hydrophobic interaction are given in a unit of Å.