Update on the Pfam5000 Strategy for Selection of StructuralGenomics Targets

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Structural Genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good financial value, and tractable. In 2003, we presented the ''Pfam5000'' strategy, which involves selecting the 5,000 most important families from the Pfam database as sources for targets. In this update, we show that although both the Pfam database and the number of sequenced genomes have increased in size, the expected benefits of the Pfam5000 strategy have not changed substantially. Solving the ... continued below

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Chandonia, John-Marc & Brenner, Steven E. June 27, 2005.

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Structural Genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good financial value, and tractable. In 2003, we presented the ''Pfam5000'' strategy, which involves selecting the 5,000 most important families from the Pfam database as sources for targets. In this update, we show that although both the Pfam database and the number of sequenced genomes have increased in size, the expected benefits of the Pfam5000 strategy have not changed substantially. Solving the structures of proteins from the 5,000 largest Pfam families would allow accurate fold assignment for approximately 65 percent of all prokaryotic proteins (covering 54 percent of residues) and 63 percent of eukaryotic proteins (42 percent of residues). Fewer than 2,300 of the largest families on this list remain to be solved, making the project feasible in the next five years given the expected throughput to be achieved in the production phase of the Protein Structure Initiative.

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  • 2005 IEEE Engineering in Medicine and Biology27th Annual Conference, Shanghai, China, September 1-4,2005

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  • Report No.: LBNL--57924
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 878532
  • Archival Resource Key: ark:/67531/metadc875221

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  • June 27, 2005

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  • Sept. 21, 2016, 2:29 a.m.

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  • Dec. 9, 2016, 10:30 p.m.

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Chandonia, John-Marc & Brenner, Steven E. Update on the Pfam5000 Strategy for Selection of StructuralGenomics Targets, article, June 27, 2005; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc875221/: accessed November 17, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.