Target Selection and Deselection at the Berkeley StructuralGenomics Center

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At the Berkeley Structural Genomics Center (BSGC), our goalis to obtain a near-complete structural complement of proteins in theminimal organisms Mycoplasma genitalium and M. pneumoniae, two closelyrelated pathogens. Current targets for structure determination have beenselected in six major stages, starting with those predicted to be mosttractable to high throughput study and likely to yield new structuralinformation. We report on the process used to select these proteins, aswell as our target deselection procedure. Target deselection reducesexperimental effort by eliminating targets similar to those recentlysolved by the structural biology community or other centers. We measurethe impact of the 69 structures solved at ... continued below

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Chandonia, John-Marc; Kim, Sung-Hou & Brenner, Steven E. March 22, 2005.

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At the Berkeley Structural Genomics Center (BSGC), our goalis to obtain a near-complete structural complement of proteins in theminimal organisms Mycoplasma genitalium and M. pneumoniae, two closelyrelated pathogens. Current targets for structure determination have beenselected in six major stages, starting with those predicted to be mosttractable to high throughput study and likely to yield new structuralinformation. We report on the process used to select these proteins, aswell as our target deselection procedure. Target deselection reducesexperimental effort by eliminating targets similar to those recentlysolved by the structural biology community or other centers. We measurethe impact of the 69 structures solved at the BSGC as of July 2004 onstructure prediction coverage of the M. pneumoniae and M. genitaliumproteomes. The number of Mycoplasma proteins for which thefold couldfirst be reliably assigned based on structures solved at the BSGC (24 M.pneumoniae and 21 M. genitalium) is approximately 25 percent of the totalresulting from work at all structural genomics centers and the worldwidestructural biology community (94 M. pneumoniae and 86M. genitalium)during the same period. As the number of structures contributed by theBSGC during that period is less than 1 percent of the total worldwideoutput, the benefits of a focused target selection strategy are apparent.If the structures of all current targets were solved, the percentage ofM. pneumoniae proteins for which folds could be reliably assigned wouldincrease from approximately 57 percent (391 of 687) at present to around80 percent (550 of 687), and the percentage of the proteome that could beaccurately modeled would increase from around 37 percent (254 of 687) toabout 64 percent (438 of 687). In M. genitalium, the percentage of theproteome that could be structurally annotated based on structures of ourremaining targets would rise from 72 percent (348 of 486) to around 76percent (371 of 486), with the percentage of accurately modeled proteinswould rise from 50 percent (243 of 486) to 58 percent (283 of 486).Sequences and data on experimental progress on our targets are availablein the public databases Target DB and PEPCdb.

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  • Journal Name: PROTEINS: Structure, Function, andBioinformatics; Journal Volume: 62; Journal Issue: 2; Related Information: Journal Publication Date: 02/01/2006

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  • Report No.: LBNL--57702
  • Grant Number: DE-AC02-05CH11231
  • Grant Number: NIH1-P50-GM62412;1K22-HG00056
  • Office of Scientific & Technical Information Report Number: 894704
  • Archival Resource Key: ark:/67531/metadc885688

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  • March 22, 2005

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  • Sept. 22, 2016, 2:13 a.m.

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  • Sept. 30, 2016, 2:42 p.m.

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Chandonia, John-Marc; Kim, Sung-Hou & Brenner, Steven E. Target Selection and Deselection at the Berkeley StructuralGenomics Center, article, March 22, 2005; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc885688/: accessed August 21, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.