OLDERADO domains and clusters

pdbe.org/nmr

Domain composition and clustering (OLDERADO)

OLDERADO provides analysis of clustering and domain composition for NMR structure ensembles. Use the search box below to access OLDERADO reports for individual PDB entries.


OLDERADO results are available for most NMR entries in the PDB, which contain protein structures. The reports include identification of the most representative model and clusters within the ensemble and determination of rigid fragments or "domains" in the structure. The OLDERADO database has been compiled using two programs: NMRCORE and NMRCLUST, originally developed at the University of Leicester. For an illustrated example click here.

NMRCORE

This program automatically defines (i) the core atoms, and (ii) the rigid body(ies) in which these lie. It uses a sorted list of dihedral angle order parameters to define the core, followed by the automatic clustering of the variances in inter-atomic 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 penalty function to automatically determine a cut-off in the clustering hierarchy. Once the models are clustered, the one closest to the centroid of the largest cluster is selected as the "most representative".

References

  • L.A. Kelley, S.P. Gardner and M.J. Sutcliffe. An Automated Approach For Clustering An Ensemble Of NMR-Derived Protein Structures Into Conformationally-Related Subfamilies. Protein Eng. (1997) 11:1063-1065 DOI: 10.1093/protein/9.11.1063
  • L.A. Kelley, S.P. Gardner and M.J. Sutcliffe. An Automated Approach For Defining Core Atoms And Domains In An Ensemble Of NMR-Derived Protein Structures. Protein Eng. (1997) 10:737-741 DOI: 10.1093/protein/10.6.737
  • L.A. Kelley and M.J. Sutcliffe. OLDERADO: On-line database of ensemble representatives and domains. Protein Sci. (1997) 6:2628-2630. DOI: 10.1002/pro.5560061215.