Proteins@home: Difference between revisions

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'''Proteins@home''' (styled ''proteins@home'') was a non-profit [[volunteer computing]] project built on the [[Berkeley Open Infrastructure for Network Computing]] (BOINC) platform.<ref name="wikipedia">{{cite encyclopedia |title=Proteins@home |encyclopedia=Wikipedia |url=https://en.wikipedia.org/wiki/Proteins@home |access-date=2026-06-08}}</ref> The project ran from December 28, 2006 to June 2008 and was operated by the Laboratoire de Biochimie (CNRS UMR 7654) in the Department of Biology at [[École Polytechnique]], located in Palaiseau, near Paris, France.<ref name="boinc-news">{{cite web |url=https://boinc.berkeley.edu/forum_thread.php?id=5136 |title=The Proteins@Home project is now open |publisher=BOINC Message Boards |date=2006-12-28 |access-date=2026-06-08}}</ref> Its scientific goal was to map the ''inverse protein folding problem'' across approximately 1,500 representative [[protein fold|protein folds]], building a database of pairwise energy functions that could be used to predict protein structure, understand protein evolution, and design new proteins with potential biomedical applications.<ref name="projdescription">{{cite web |url=https://web.archive.org/web/20070601000000*/http://biology.polytechnique.fr/proteinsathome/ |title=proteins@home |publisher=Wayback Machine |access-date=2026-06-08}}</ref>

[[File:Protein-structure.png|thumb|250px|right|The four levels of protein structure — from the primary amino-acid sequence through to a tertiary fold. The relationship between sequence and fold was at the heart of the Proteins@home project.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Protein-structure.png |title=File:Protein-structure.png |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]

== Background ==

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=== Launch and operation ===

[[File:Ecole Polytechnique France seen from lake DSC03389.JPG|thumb|250px|left|The campus of [[École Polytechnique]] at Palaiseau, France, home of the Laboratoire de Biochimie (CNRS UMR 7654) that ran Proteins@home.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Ecole_Polytechnique_France_seen_from_lake_DSC03389.JPG |title=File:Ecole Polytechnique France seen from lake DSC03389.JPG |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]

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."<ref name="boinc-news"/> Volunteers could register and download the BOINC client to begin donating CPU cycles to the project.

[[File:Ecole Polytechnique France seen from lake DSC03389.JPG|thumb|250px|left|The campus of [[École Polytechnique]] at Palaiseau, France, home of the Laboratoire de Biochimie (CNRS UMR 7654) that ran Proteins@home.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Ecole_Polytechnique_France_seen_from_lake_DSC03389.JPG |title=File:Ecole Polytechnique France seen from lake DSC03389.JPG |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]

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.<ref name="bmc2008">{{cite journal |last1=Schmidt am Busch |first1=Marcel |last2=Lopes |first2=Anne |last3=Amara |first3=Najette |last4=Bathelt |first4=Christine |last5=Simonson |first5=Thomas |date=2008-03-13 |title=Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design |journal=BMC Bioinformatics |volume=9 |page=148 |doi=10.1186/1471-2105-9-148 |pmid=18366628 |pmc=2292695}}</ref><ref name="proteus">{{cite web |url=https://proteus.polytechnique.fr/ |title=The Proteus software for computational protein design |publisher=École Polytechnique |access-date=2026-06-08}}</ref>

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During its operational period, the Proteins@home distributed computing platform was used by volunteers in over 100 countries.<ref name="plosone2010">{{cite journal |last1=Schmidt am Busch |first1=Marcel |last2=Sedano |first2=Audrey |last3=Simonson |first3=Thomas |date=2010-05-05 |title=Computational Protein Design: Validation and Possible Relevance as a Tool for Homology Searching and Fold Recognition |journal=PLOS ONE |volume=5 |issue=5 |page=e10410 |doi=10.1371/journal.pone.0010410 |pmid=20463972 |pmc=2864755}}</ref>

=== Computational methodology ===

[[File:Protein Structure Gif.gif|thumb|380x380px|A rotating 3D protein structure, illustrating the kind of tertiary fold geometry that Proteins@home worked to map using distributed volunteer computing.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Protein_Structure_Gif.gif |title=File:Protein Structure Gif.gif |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]

Each work unit sent to a volunteer computer contained the structural coordinates of one or more protein backbone templates drawn from a representative subset of the [[Structural Classification of Proteins]] (SCOP) database. For each template, the XPLOR molecular modelling program was used to precompute the pairwise interaction energy between all pairs of residue positions, considering all possible amino acid types and [[rotamer]] conformations at each position.<ref name="plosone2010"/>

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== Scientific publications ==

[[File:Protein-structure.png|thumb|518x518px|The four levels of protein structure — from the primary amino-acid sequence through to a tertiary fold. The relationship between sequence and fold was at the heart of the Proteins@home project.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Protein-structure.png |title=File:Protein-structure.png |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]

The Proteins@home computing platform directly enabled several peer-reviewed publications from the Simonson group.

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The insights and code base from Proteins@home fed directly into the '''Proteus''' software package, developed by the same group at École Polytechnique and their collaborators.<ref name="proteus"/> Proteus extended the pairwise decomposition framework with additional energy terms including generalised Born solvation, Monte Carlo simulation at constant pH, and improved rotamer libraries, and has been applied to problems such as enzyme active site redesign and aminoacyl-tRNA synthetase specificity engineering. The first full description of Proteus was published in the ''Journal of Computational Chemistry'' in 2013.<ref>{{cite journal |last1=Simonson |first1=Thomas |last2=Gaillard |first2=Thomas |last3=Mignon |first3=David |last4=Schmidt am Busch |first4=Marcel |last5=Lopes |first5=Anne |last6=Amara |first6=Najette |last7=Polydorides |first7=Savvas |last8=Sedano |first8=Audrey |last9=Druart |first9=Karen |last10=Archontis |first10=Georgios |year=2013 |title=Computational protein design: the Proteus software and selected applications |journal=Journal of Computational Chemistry |volume=34 |issue=28 |pages=2472–2484 |doi=10.1002/jcc.23418 |pmid=24038178}}</ref>

[[File:Protein Structure Gif.gif|thumb|250px|right|A rotating 3D protein structure, illustrating the kind of tertiary fold geometry that Proteins@home worked to map using distributed volunteer computing.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Protein_Structure_Gif.gif |title=File:Protein Structure Gif.gif |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]

== See also ==

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 '''Proteins@home''' (styled ''proteins@home'') was a non-profit [[volunteer computing]] project built on the [[Berkeley Open Infrastructure for Network Computing]] (BOINC) platform.<ref name="wikipedia">{{cite encyclopedia |title=Proteins@home |encyclopedia=Wikipedia |url=https://en.wikipedia.org/wiki/Proteins@home |access-date=2026-06-08}}</ref> The project ran from December 28, 2006 to June 2008 and was operated by the Laboratoire de Biochimie (CNRS UMR&nbsp;7654) in the Department of Biology at [[École Polytechnique]], located in Palaiseau, near Paris, France.<ref name="boinc-news">{{cite web |url=https://boinc.berkeley.edu/forum_thread.php?id=5136 |title=The Proteins@Home project is now open |publisher=BOINC Message Boards |date=2006-12-28 |access-date=2026-06-08}}</ref> Its scientific goal was to map the ''inverse protein folding problem'' across approximately 1,500 representative [[protein fold|protein folds]], building a database of pairwise energy functions that could be used to predict protein structure, understand protein evolution, and design new proteins with potential biomedical applications.<ref name="projdescription">{{cite web |url=https://web.archive.org/web/20070601000000*/http://biology.polytechnique.fr/proteinsathome/ |title=proteins@home |publisher=Wayback Machine |access-date=2026-06-08}}</ref>
-[[File:Protein-structure.png|thumb|250px|right|The four levels of protein structure — from the primary amino-acid sequence through to a tertiary fold. The relationship between sequence and fold was at the heart of the Proteins@home project.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Protein-structure.png |title=File:Protein-structure.png |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]
 == Background ==
@@ Line 42: / Line 40: @@
 === Launch and operation ===
+[[File:Ecole Polytechnique France seen from lake DSC03389.JPG|thumb|250px|left|The campus of [[École Polytechnique]] at Palaiseau, France, home of the Laboratoire de Biochimie (CNRS UMR 7654) that ran Proteins@home.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Ecole_Polytechnique_France_seen_from_lake_DSC03389.JPG |title=File:Ecole Polytechnique France seen from lake DSC03389.JPG |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]
 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."<ref name="boinc-news"/> Volunteers could register and download the BOINC client to begin donating CPU cycles to the project.
-[[File:Ecole Polytechnique France seen from lake DSC03389.JPG|thumb|250px|left|The campus of [[École Polytechnique]] at Palaiseau, France, home of the Laboratoire de Biochimie (CNRS UMR 7654) that ran Proteins@home.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Ecole_Polytechnique_France_seen_from_lake_DSC03389.JPG |title=File:Ecole Polytechnique France seen from lake DSC03389.JPG |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]
 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&nbsp;7654), Department of Biology, École Polytechnique, 91128 Palaiseau, France.<ref name="bmc2008">{{cite journal |last1=Schmidt am Busch |first1=Marcel |last2=Lopes |first2=Anne |last3=Amara |first3=Najette |last4=Bathelt |first4=Christine |last5=Simonson |first5=Thomas |date=2008-03-13 |title=Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design |journal=BMC Bioinformatics |volume=9 |page=148 |doi=10.1186/1471-2105-9-148 |pmid=18366628 |pmc=2292695}}</ref><ref name="proteus">{{cite web |url=https://proteus.polytechnique.fr/ |title=The Proteus software for computational protein design |publisher=École Polytechnique |access-date=2026-06-08}}</ref>
@@ Line 52: / Line 50: @@
 During its operational period, the Proteins@home distributed computing platform was used by volunteers in over 100 countries.<ref name="plosone2010">{{cite journal |last1=Schmidt am Busch |first1=Marcel |last2=Sedano |first2=Audrey |last3=Simonson |first3=Thomas |date=2010-05-05 |title=Computational Protein Design: Validation and Possible Relevance as a Tool for Homology Searching and Fold Recognition |journal=PLOS ONE |volume=5 |issue=5 |page=e10410 |doi=10.1371/journal.pone.0010410 |pmid=20463972 |pmc=2864755}}</ref>
 === Computational methodology ===
+[[File:Protein Structure Gif.gif|thumb|380x380px|A rotating 3D protein structure, illustrating the kind of tertiary fold geometry that Proteins@home worked to map using distributed volunteer computing.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Protein_Structure_Gif.gif |title=File:Protein Structure Gif.gif |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]
 Each work unit sent to a volunteer computer contained the structural coordinates of one or more protein backbone templates drawn from a representative subset of the [[Structural Classification of Proteins]] (SCOP) database. For each template, the XPLOR molecular modelling program was used to precompute the pairwise interaction energy between all pairs of residue positions, considering all possible amino acid types and [[rotamer]] conformations at each position.<ref name="plosone2010"/>
@@ Line 76: / Line 77: @@
 == Scientific publications ==
+[[File:Protein-structure.png|thumb|518x518px|The four levels of protein structure — from the primary amino-acid sequence through to a tertiary fold. The relationship between sequence and fold was at the heart of the Proteins@home project.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Protein-structure.png |title=File:Protein-structure.png |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]
 The Proteins@home computing platform directly enabled several peer-reviewed publications from the Simonson group.
@@ Line 96: / Line 99: @@
 The insights and code base from Proteins@home fed directly into the '''Proteus''' software package, developed by the same group at École Polytechnique and their collaborators.<ref name="proteus"/> Proteus extended the pairwise decomposition framework with additional energy terms including generalised Born solvation, Monte Carlo simulation at constant pH, and improved rotamer libraries, and has been applied to problems such as enzyme active site redesign and aminoacyl-tRNA synthetase specificity engineering. The first full description of Proteus was published in the ''Journal of Computational Chemistry'' in 2013.<ref>{{cite journal |last1=Simonson |first1=Thomas |last2=Gaillard |first2=Thomas |last3=Mignon |first3=David |last4=Schmidt am Busch |first4=Marcel |last5=Lopes |first5=Anne |last6=Amara |first6=Najette |last7=Polydorides |first7=Savvas |last8=Sedano |first8=Audrey |last9=Druart |first9=Karen |last10=Archontis |first10=Georgios |year=2013 |title=Computational protein design: the Proteus software and selected applications |journal=Journal of Computational Chemistry |volume=34 |issue=28 |pages=2472–2484 |doi=10.1002/jcc.23418 |pmid=24038178}}</ref>
-[[File:Protein Structure Gif.gif|thumb|250px|right|A rotating 3D protein structure, illustrating the kind of tertiary fold geometry that Proteins@home worked to map using distributed volunteer computing.<ref>{{cite web |url=https://commons.wikimedia.org/wiki/File:Protein_Structure_Gif.gif |title=File:Protein Structure Gif.gif |publisher=Wikimedia Commons |access-date=2026-06-08}}</ref>]]
 == See also ==