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| Title: | Automatic target selection for structural genomics on eukaryotes |
| Author: | Jinfeng Liu, Hedi Hegyi, Thomas B Acton, Gaetano T Montelione, & Burkhard Rost |
| Quote: | Proteins, 2004, 56(2):188-200 |
A central goal of structural genomics is to experimentally determine representative structures for all protein families. At least 14 structural genomics pilot projects are currently investigating the feasibility of high-throughput structure determination; nine of these in the USA are NIH funded. Initiatives differ in the particular subset of 'all families' on which they focus. At the NorthEast Structural Genomics consortium (NESG), we target eukaryotic protein domain families. The automatic target selection procedure has three aims: (1) Identify all protein domain families from currently five entirely sequenced eukaryotic target organisms based on their sequence homology. (2) Discard those families that can be modelled based on structural information already present in the PDB. (3) Target representatives of the remaining families for structure determination. In order to guarantee that all members of one family share a common fold-like region, we had to begin by dissecting proteins into structural domain-like regions before clustering. Our hierarchical approach, CHOP, utilising homology to PrISM, Pfam-A, and SWISS-PROT chopped the 103,796 eukaryotic proteins/ORFs into 247,222 fragments. 122,999 of these fragments appeared suitable targets that were grouped into over 27,000 singleton and over 18,000 multi-fragment clusters. Thus, our results suggested that it might be necessary to determine over 40,000 structures to minimally cover the subset of five eukaryotic proteomes.