How is the Database Generated? (see Publication)

The database has been generated by two analysis tools: NMRCORE and NMRCLUST. The OLDERADO service was developed in Mike Sutcliffe's group by Lawrence Kelley . Default parameters were used for each structure.

NMRCORE

This program automatically defines (i) the core atoms, and (ii) the rigid body(ies) in which these lie. NMRCORE uses a sorted list of dihedral angle order parameters to define the core, followed by the automatic clustering of the variances in inter-atom distances to define the rigid body(ies) which comprise the core.

NMRCLUST

This program automatically clusters ensemble members into conformationally-related sub-families. All structures are superposed in a pairwise manner and the resulting R.M.S. distance between each pair calculated. For an ensemble with N members, this results in an NxN matrix of R.M.S. values. This matrix is used as a similarity score on which to base the clustering. Average linkage cluster analysis is used in conjunction with a novel penalty function to determine a cut-off in the clustering hierarchy automatically.

Once clustered, a single "most representative" structure is selected. This is the structure closest to the centroid of the largest cluster. This is the representative structure.

For a graphical idea of how these analysis tools work, visit the EXAMPLE page

Acknowledgements