Human Proteome Folding Project Explained
The Human Proteome Folding Project (HPF) is a collaborative effort between New York University (Bonneau Lab), the Institute for Systems Biology (ISB) and the University of Washington (Baker Lab), using the Rosetta software developed by the Rosetta Commons. The project is managed by the Bonneau lab.
HPF Phase 1 applied Rosetta v4.2x software on the human genome and 89 others, starting in November 2004. Phase 1 ended in July 2006. HPF Phase 2 (HPF2) applies the Rosetta v4.8x software in higher resolution, "full atom refinement" mode, concentrating on cancer biomarkers (proteins found at dramatically increased levels in cancer tissues), human secreted proteins and malaria.
Phase 1 ran on two volunteer computing grids: on United Devices' grid.org, and on the World Community Grid, an IBM philanthropic initiative. Phase 2 of the project ran exclusively on the World Community Grid; it terminated in 2013 after more than 9 years of IBM involvement.
The Institute for Systems Biology will use the results of the computations within its larger research efforts.
Publications
- Drew . K . Winters . P . Butterfoss . GL . Berstis . V . Uplinger . K . Armstrong . J . Riffle . M . Schweighofer . E . Bovermann . B . Goodlett . DR . Davis . TN . Shasha . D . Malmström . L . Bonneau . R . The Proteome Folding Project: proteome-scale prediction of structure and function. . Genome Research . November 2011 . 21 . 11 . 1981–94 . 10.1101/gr.121475.111 . 21824995. 3205581 . free .
- Baltz . AG . Munschauer . M . Schwanhäusser . B . Vasile . A . Murakawa . Y . Schueler . M . Youngs . N . Penfold-Brown . D . Drew . K . Milek . M . Wyler . E . Bonneau . R . Selbach . M . Dieterich . C . Landthaler . M . The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. . Molecular Cell . 8 June 2012 . 46 . 5 . 674–90 . 10.1016/j.molcel.2012.05.021 . 22681889. free . (Used fold enrichment and function predictions)
- Wang . KH . Isidro . AL . Domingues . L . Eskandarian . HA . McKenney . PT . Drew . K . Grabowski . P . Chua . MH . Barry . SN . Guan . M . Bonneau . R . Henriques . AO . Eichenberger . P . The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis. . Molecular Microbiology . November 2009 . 74 . 3 . 634–49 . 10.1111/j.1365-2958.2009.06886.x . 19775244. 2806667 . free . (Used predictions as hypothesis for further experimental characterization)
See also
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