proteins@home
proteins@home (sometimes styled Proteins@Home) was a volunteer computing project built on the BOINC platform. It was operated by the Department of Biology at École Polytechnique in Palaiseau, France, and ran from December 2006 until June 2008.[1] The project harnessed the idle processing time of volunteers' computers to help solve the inverse protein folding problem: given a protein's three-dimensional fold, which amino acid sequences are compatible with that shape.[1]
History
proteins@home was announced as open to volunteers in an official BOINC project listing that described it as a large-scale protein structure prediction project based at the École Polytechnique in Paris.[2] According to Wikipedia, the project began operation on December 28, 2006, and concluded in June 2008.[1] A snapshot of the project's home page was archived by the Wayback Machine on March 15, 2007, while the project was still in its early phase.[3] The project's official listing was also maintained on the BOINC project wiki.[4]
The project was led by Thomas Simonson of the Laboratoire de Biochimie (UMR CNRS 7654) at École Polytechnique, with Marcel Schmidt am Busch as the principal researcher coordinating the volunteer computation.[5] At its peak the project drew on computers from several thousand volunteers in more than 100 countries.[5]
Launch and operation
proteins@home was formally announced as open on December 28, 2006, when BOINC project administrator David Anderson posted on the BOINC message boards that the project was "now open" and "based at the École Polytechnique in Paris."[6] Volunteers could register and download the BOINC client to begin donating CPU cycles to the project.
The research team was led by Thomas Simonson, with contributions from Marcel Schmidt am Busch, Anne Lopes, David Mignon, Thomas Gaillard, Najette Amara, and Christine Bathelt, all based at the Laboratoire de Biochimie (CNRS UMR 7654), Department of Biology, École Polytechnique, 91128 Palaiseau, France.[7][8]
The BOINC news feed recorded on February 7, 2008 that "proteins@Home has resumed operations",[9] indicating a temporary interruption before the project reopened to participants. The project concluded in June 2008.
During its operational period, the proteins@home distributed computing platform was used by volunteers in over 100 countries.[10]
About the project
The scientific goal of proteins@home was to help solve the inverse protein folding problem: while a protein's amino acid sequence determines its three-dimensional fold, many different sequences can in principle be compatible with a given fold. The project aimed to enumerate plausible sequences for a representative set of roughly 1,500 known protein folds.[1]
The most computationally expensive step was building a database of pairwise energy functions describing the interactions between amino acid side chains at each structural position. Because these energy terms could be expressed as sums over pairs of interacting residues, the total energy of a candidate sequence could be decomposed as
where is the self-energy of the side chain at position and is the pairwise interaction energy between positions and . This additive structure meant the expensive pairwise terms could be precomputed once and distributed across volunteer machines, making the calculation tractable at scale.[5] Once the energy database was built, researchers could rapidly explore the space of amino acid sequences for a given fold and retain the most energetically favorable candidates, with applications to protein structure prediction, the study of protein evolution, and the design of new proteins.[1]
Screensaver
Like other BOINC-based projects, proteins@home shipped with a graphical screensaver that ran while a volunteer's computer was otherwise idle, visualizing the state of the client's current work unit.
Legacy
proteins@home is no longer active; its official BOINC statistics are unavailable following the project's shutdown in mid-2008. The project's official website, biology.polytechnique.fr/proteinsathome, is no longer online and is preserved only through the Internet Archive's Wayback Machine.[3] The computational protein design methodology developed for the project, including its pairwise-decomposable energy model, continued to be used and refined by the same research group in subsequent studies.[11]
Publications
The following papers are listed on the official BOINC publications page as scientific results arising from HashClash's BOINC-based computing.
- Schmidt am Busch, Marcel, Audrey Sedano and Thomas Simonson. Computational Protein Design: Validation and Possible Relevance as a Tool for Homology Searching and Fold Recognition. PLoS ONE (2010). DOI: 10.1371/journal.pone.0010410.
- Schmidt am Busch, Marcel, David Mignon and Thomas Simonson. Computational protein design as a tool for fold recognition. Proteins: Structure, Function, and Bioinformatics (2009). DOI: 10.1002/prot.22426.
- Schmidt Am Busch, Marcel, Anne Lopes, David Mignon and Thomas Simonson. Computational protein design: Software implementation, parameter optimization, and performance of a simple model. Journal of Computational Chemistry (2008). DOI: 10.1002/jcc.20870.[11]
- am Busch, Marcel Schmidt, Anne Lopes, Najette Amara, Christine Bathelt and Thomas Simonson. Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. BMC Bioinformatics (2008). DOI: 10.1186/1471-2105-9-148.
- Schmidt am Busch, Marcel, Anne Lopes, David Mignon, Thomas Gaillard and Thomas Simonson. The Inverse Protein Folding Problem: Protein Design and Structure Prediction in the Genomic Era. In: Zeng, J., Zhang, R.-Q. and Treutlein, H. (eds.), Quantum Simulations of Materials and Biological Systems, Springer, Dordrecht (2012), pp. 121–140. DOI: 10.1007/978-94-007-4948-1_7.
See also
References
- ↑ 1.0 1.1 1.2 1.3 1.4 proteins@home. Wikipedia. Retrieved 2026-07-05.
- ↑ BOINC project news archive. BOINC-site GitHub repository. BOINC. Retrieved 2026-07-05.
- ↑ 3.0 3.1 proteins@home. Wayback Machine. Retrieved 2026-07-05.
- ↑ Proteins@Home. BOINC wiki. University of California, Berkeley. Retrieved 2026-07-05.
- ↑ 5.0 5.1 5.2 (2010).Computational Protein Design: Validation and Possible Relevance as a Tool for Homology Searching and Fold Recognition. PLoS ONE. pp. e10410. DOI: 10.1371/journal.pone.0010410.
- ↑ https://boinc.berkeley.edu/forum_thread.php?id=5136
- ↑ (2008-03-13).Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. BMC Bioinformatics. DOI: 10.1186/1471-2105-9-148.
- ↑ The Proteus software for computational protein design. École Polytechnique. Retrieved 2026-06-08.
- ↑ boinc_news.php (BOINC site source). GitHub / BOINC. Retrieved 2026-06-08.
- ↑ (2010-05-05).Computational Protein Design: Validation and Possible Relevance as a Tool for Homology Searching and Fold Recognition. PLOS ONE. DOI: 10.1371/journal.pone.0010410.
- ↑ 11.0 11.1 (2008-05-29).Computational protein design: Software implementation, parameter optimization, and performance of a simple model. Journal of Computational Chemistry. pp. 1092–1102. DOI: 10.1002/jcc.20870.