Protein folds were identified by a consensus approach of three popular fold / domain classification systems: structural classification of proteins (SCOP) v1.65 [1]; class, architecture, topology, and homologous superfamily (CATH) v2.4 [2]; and the Dali Domain Dictionary v3.1β [3] as described previously [4]. In that work, a non-redundant list of protein structures was sorted to determine the populations of the common fold groups. For each fold, potential protein targets’ structures were selected from the PDB. Selection criteria were such that single chains were preferred over multimers and multi-domain proteins, shorter chains were preferred over longer ones, and high resolution crystal structures were preferred over those of lower resolution and those derived from NMR. Finally, for each fold, the list of suitable protein target structures was reduced by selecting for those systems with available experimental data in the forms of NMR observables, folding and unfolding studies, drug design, or protein interaction.

References

1. Murzin, A.G., et al., Scop - a Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology, 1995. 247(4): p. 536-540.
2. Orengo, C.A., et al., CATH - a hierarchic classification of protein domain structures. Structure, 1997. 5(8): p. 1093-1108.
3. Dietmann, S., et al., A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Research, 2001. 29(1): p. 55-57.
4. Day, R., et al., A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary. Protein Science, 2003. 12(10): p. 2150-2160.