Figure - PMC

Skip to main content

View full-text article in PMC

. Author manuscript; available in PMC: 2010 Oct 29.

Published in final edited form as: J Phys Chem B. 2009 Oct 29;113(43):14343–14354. doi: 10.1021/jp907375b

Plots of RMSD from experiment for the peptide heavy atoms versus energy for 40 2-ns simulated annealing cycling simulations using the ε(r)=4r model. Half of the trajectories were started from the crystal structure and half from the extended conformation on the protein surface. These plots include only structures near local energy minima obtained below 5 K. a1 to a6 are the results for the PTP-peptide, YopH-peptide, PTK-peptide, IGF-peptide, PKA-peptide, and CDK-peptide systems respectively using Energy Model I. b1 to b6 are similar except using Energy Model II to score the structures. (Energy Model I used the total energy of the whole system; Energy Model II excluded the energy of the protein.)

Plots of RMSD from experiment for the peptide heavy atoms versus energy for 40 2-ns simulated annealing cycling simulations using the ε(r)=4r model. Half of the trajectories were started from the crystal structure and half from the extended conformation on the protein surface. These plots include only structures near local energy minima obtained below 5 K. a1 to a6 are the results for the PTP-peptide, YopH-peptide, PTK-peptide, IGF-peptide, PKA-peptide, and CDK-peptide systems respectively using Energy Model I. b1 to b6 are similar except using Energy Model II to score the structures. (Energy Model I used the total energy of the whole system; Energy Model II excluded the energy of the protein.)