Fig. 2
From: PDB-Explorer: a web-based interactive map of the protein data bank in shape space
Retrieval of conformer analogs from the MD trajectory of a 24 residue peptide by 3DP similarity. a ROC curve for retrieving structures with RMSD < 2 Å, relative the last frame in a 50 ns MD simulation taken as reference, by 3DP similarity (blue) and by random selection (red), averaged over 50 different MD simulations. b Recovery of structures with RMSD < 2 Å to the reference (blue) and all structures (red) as function of CBD3DP from the reference. The structure alignment and RMSD calculation of all heavy atoms were carried out with the AMBER12 package. The sequence of the 24-mer peptide is MKKRLAYAIIQFLHDQLRHGGLSS