{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T05:33:35Z","timestamp":1766468015051},"reference-count":61,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2005,11,7]],"date-time":"2005-11-07T00:00:00Z","timestamp":1131321600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2006,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>At the Berkeley Structural Genomics Center (BSGC), our goal is to obtain a near\u2010complete structural complement of proteins in the minimal organisms <jats:italic>Mycoplasma genitalium<\/jats:italic> and <jats:italic>M. pneumoniae<\/jats:italic>, two closely related pathogens. Current targets for structure determination have been selected in six major stages, starting with those predicted to be most tractable to high throughput study and likely to yield new structural information. We report on the process used to select these proteins, as well as our target deselection procedure. Target deselection reduces experimental effort by eliminating targets similar to those recently solved by the structural biology community or other centers. We measure the impact of the 69 structures solved at the BSGC as of July 2004 on structure prediction coverage of the <jats:italic>M. pneumoniae<\/jats:italic> and <jats:italic>M. genitalium<\/jats:italic> proteomes. The number of <jats:italic>Mycoplasma<\/jats:italic> proteins for which the fold could first be reliably assigned based on structures solved at the BSGC (24 <jats:italic>M. pneumoniae<\/jats:italic> and 21 <jats:italic>M. genitalium<\/jats:italic>) is approximately 25% of the total resulting from work at all structural genomics centers and the worldwide structural biology community (94 <jats:italic>M. pneumoniae<\/jats:italic> and 86 <jats:italic>M. genitalium<\/jats:italic>) during the same period. As the number of structures contributed by the BSGC during that period is less than 1% of the total worldwide output, the benefits of a focused target selection strategy are apparent. If the structures of all current targets were solved, the percentage of <jats:italic>M. pneumoniae<\/jats:italic> proteins for which folds could be reliably assigned would increase from approximately 57% (391 of 687) at present to around 80% (550 of 687), and the percentage of the proteome that could be accurately modeled would increase from around 37% (254 of 687) to about 64% (438 of 687). In <jats:italic>M. genitalium<\/jats:italic>, the percentage of the proteome that could be structurally annotated based on structures of our remaining targets would rise from 72% (348 of 486) to around 76% (371 of 486), with the percentage of accurately modeled proteins would rise from 50% (243 of 486) to 58% (283 of 486). Sequences and data on experimental progress on our targets are available in the public databases TargetDB and PEPCdb. Proteins 2006. \u00a9 2005 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.20674","type":"journal-article","created":{"date-parts":[[2005,11,16]],"date-time":"2005-11-16T18:18:27Z","timestamp":1132165107000},"page":"356-370","source":"Crossref","is-referenced-by-count":23,"title":["Target selection and deselection at the Berkeley Structural Genomics Center"],"prefix":"10.1002","volume":"62","author":[{"given":"John\u2010Marc","family":"Chandonia","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sung\u2010Hou","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven 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