After a UNRES-Dock MREMD run is accomplished, the same data as for reguler MREMD run is shown: a table showing replica-exchange statistics (a), plots of histograms of UNRES energy for each temperature (b), a plot of energy vs. temperature (c), a temperature-colored scatter plot of energy vs. RMSD (d), and the temperature-colored cumulative plot of rmsd vs. step number for all replicas (e), and a cumulative plot of walk of the replicas in temperature space (f). The colors corresponding to replica temperatures are shown in panel (c), while different replicas are colored from black to yellow in panel (f).

(a) (b) (c) (d) (e) (f)

The weighted histogram analysis method (WHAM) is applied to compute the probabilities of the obtained complexes to occur at particular temperatures and, consequently, the plots of heat capacity (g) and ensemble-averaged RMSD (h) as functions of temperature; these are shown in the respective graphs.

(g) (h)

Note! Panels are labeled in this tutorial only and labels are not displayed in the outputs from real server jobs.

Finally, cluster analysis is performed to select 5 families of complexes, and representative model from each family is converted to all-atom structure and refined. Models are shown using NGL Viewer. PDB files can be downloaded by clicking on the Download button.

DockQ is utilised to measure quality of 5 docked models.

Only sequence is given for the peptide. No reference structure is provided for the complex.
All temperatures are multiplexed, total number of replicas is 36.

After a UNRES-Dock MREMD run is accomplished without the reference structure, a table showing replica-exchange statistics (a), plots of histograms of UNRES energy for each temperature (b), a plot of energy vs. temperature (c), and a cumulative plot of walk of the replicas in temperature space (d) are displayed. The colors corresponding to replica temperatures are shown in panel (c), while different replicas are colored from black to yellow in panel (d).

(a) (b) (c) (d)

The weighted histogram analysis method (WHAM) is applied to compute the probabilities of the obtained complexes to occur at particular temperatures and, consequently, the plot of heat capacity (e) as a functions of temperature is shown.

(e)

Note! Panels are labeled in this tutorial only and labels are not displayed in the outputs from real server jobs.

Finally cluster analysis is performed to select 10 families of conformations, and representative model from each family is converted to all-atom structure and refined. Models are shown using NGL Viewer. PDB files can be downloaded by clicking on the Download button.