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{{Infobox software
{{Infobox software
| name                = proteins@home
| name                = proteins@home
| logo                =
| logo caption        =
| screenshot          = Proteins.gif
| screenshot          = Proteins.gif
| caption              = The proteins@home screensaver, visualising a rotating protein structure
| caption              = The proteins@home screensaver
| description          = proteins@home was a completed Biochemistry BOINC project that tackled the inverse protein folding problem, operated by the Laboratoire de Biochimie at École Polytechnique, Palaiseau, France, from December 2006 to June 2008.
| description          = proteins@home was a completed BOINC volunteer computing project run by the Department of Biology at École Polytechnique that used donated computer time to build a database of protein energy functions in support of computational protein design and the inverse protein folding problem.
 
| status              = Completed
| status              = Completed
| category            = Biochemistry
| category            = Biochemistry
| compute              = CPU
| compute              = CPU
| dependencies        = None
| dependencies        = None
 
| developer            = Department of Biology, École Polytechnique
| developer            = Thomas Simonson et al., École Polytechnique
| author              = Thomas Simonson
| author              = Thomas Simonson
| sponsor              = Laboratoire de Biochimie (CNRS UMR 7654), École Polytechnique
| sponsor              = École Polytechnique
| maintainer          = Marcel Schmidt am Busch
| released            = {{Start date and age|2006|12|28}}
| released            = {{Start date and age|2006|12|28}}
| completed            = June 2008
| completed            = June 2008
 
| discontinued        =
| repository          =
| programming language =
| operating system    = Windows, Linux, macOS
| operating system    = Windows, Linux, macOS
 
| size                =
| stats as of          =
| average performance  =
| active users        =
| total users          =
| active hosts        =
| total hosts          =
| rac                  =
| credit per day      =
| gpu performance      =
| cpu performance      =
| website              = {{URL|http://biology.polytechnique.fr/proteinsathome/}} {{small|(archived)}}
| website              = {{URL|http://biology.polytechnique.fr/proteinsathome/}} {{small|(archived)}}
| license              =
}}
}}


{{Lowercase title}}
{{Lowercase title}}


'''[https://web.archive.org/web/20070306022756/http://biology.polytechnique.fr/proteinsathome/ 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>
'''[https://web.archive.org/web/20070306022756/http://biology.polytechnique.fr/proteinsathome/ proteins@home]''' (sometimes styled ''Proteins@Home'') was a [[wikipedia:Volunteer computing|volunteer computing]] project built on the [[wikipedia:Berkeley Open Infrastructure for Network Computing|BOINC]] platform. It was operated by the Department of Biology at [[wikipedia:École Polytechnique|École Polytechnique]] in Palaiseau, France, and ran from December 2006 until June 2008.<ref name="wp">{{Cite web |title=proteins@home |url=https://en.wikipedia.org/wiki/Proteins@home |website=Wikipedia |access-date=2026-07-05}}</ref> 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.<ref name="wp" />
 
== Background ==
 
=== Protein folding and the inverse problem ===
 
Every [[protein]] is a chain of [[amino acid]]s. The linear sequence of the chain — the ''primary structure'' — ultimately determines the protein's three-dimensional shape, or ''fold''. Formally, a protein of length <math>n</math> has a primary structure <math>s = (a_1, a_2, \ldots, a_n)</math> where each <math>a_i</math> belongs to the set of 20 standard amino acids. The chain folds by minimising its free energy, which includes contributions from electrostatics, van der Waals forces, and interactions with the solvent.
 
The ''inverse'' of this prediction problem asks: given a known three-dimensional fold, which amino acid sequences are compatible with it? This is known as the '''inverse protein folding problem''' or '''computational protein design''' (CPD). It has applications in understanding protein evolution, identifying stabilising mutations, and engineering entirely new proteins for biomedical or industrial purposes.
 
A key feature that made the problem tractable for distributed computing is that the energy can be expressed as a sum over all pairs of residue positions:
 
:<math>E_\text{total} = \sum_{i < j} E(a_i, r_i,\, a_j, r_j)</math>


where <math>E(a_i, r_i, a_j, r_j)</math> is the pairwise interaction energy between amino acid types <math>a_i</math> and <math>a_j</math> at positions <math>i</math> and <math>j</math> in rotamer conformations <math>r_i</math> and <math>r_j</math>. Because each pairwise term is independent of all others, the energy table can be precomputed in parallel across thousands of volunteer computers with almost no communication required.<ref name="jcc2008">{{cite journal |last1=Schmidt Am Busch |first1=Marcel |last2=Lopes |first2=Anne |last3=Mignon |first3=David |last4=Simonson |first4=Thomas |date=2008-05-29 |title=Computational protein design: software implementation, parameter optimization, and performance of a simple model |journal=Journal of Computational Chemistry |volume=29 |issue=7 |pages=1092–1102 |doi=10.1002/jcc.20870 |pmid=18069664 |issn=1096-987X |s2cid=890739}}</ref>
[[File:Ecole Polytechnique France seen from lake DSC03389.JPG|thumb|right|The École Polytechnique campus in Palaiseau, France, where proteins@home was based]]


== Project description ==
== 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.<ref name="boincnews">{{Cite web |title=BOINC project news archive |url=https://github.com/BOINC/boinc-site/blob/master/boinc_news.php |website=BOINC-site GitHub repository |publisher=BOINC |access-date=2026-07-05}}</ref> According to Wikipedia, the project began operation on December 28, 2006, and concluded in June 2008.<ref name="wp" /> 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.<ref name="wayback">{{Cite web |title=proteins@home |url=https://web.archive.org/web/20070315023303/http://biology.polytechnique.fr/proteinsathome |website=Wayback Machine |archive-url=https://web.archive.org/web/20070315023303/http://biology.polytechnique.fr/proteinsathome |archive-date=2007-03-15 |access-date=2026-07-05}}</ref> The project's official listing was also maintained on the [[wikipedia:BOINC|BOINC]] project wiki.<ref name="boincwiki">{{Cite web |title=Proteins@Home |url=https://boinc.berkeley.edu/wiki/Proteins@Home |website=BOINC wiki |publisher=University of California, Berkeley |access-date=2026-07-05}}</ref>


[[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 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.<ref name="plos">{{Cite journal |last1=Schmidt am Busch |first1=Marcel |last2=Sedano |first2=Audrey |last3=Simonson |first3=Thomas |title=Computational Protein Design: Validation and Possible Relevance as a Tool for Homology Searching and Fold Recognition |journal=PLoS ONE |volume=5 |issue=5 |pages=e10410 |date=2010 |doi=10.1371/journal.pone.0010410 |url=https://dx.plos.org/10.1371/journal.pone.0010410}}</ref> At its peak the project drew on computers from several thousand volunteers in more than 100 countries.<ref name="plos" />


=== Launch and operation ===
=== 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."<ref name="boinc-news"/> Volunteers could register and download the BOINC client to begin donating CPU cycles to the project.
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>https://boinc.berkeley.edu/forum_thread.php?id=5136</ref> 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&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>
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>
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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>
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>
== 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.<ref name="wp" />


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 <math>\sigma</math> could be decomposed as


=== Computational methodology ===
<math>E(\sigma) = \sum_{i} E_i(\sigma_i) + \sum_{i<j} E_{ij}(\sigma_i, \sigma_j)</math>
 
[[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"/>
 
The interaction energy used a classical molecular mechanics model that combined a Coulomb electrostatics term with an accessible surface area (ASA) implicit solvation correction. Protein stability was estimated by comparing the energy of the folded state to that of an extended, unfolded-state model constructed from a library of tripeptide structures.<ref name="bmc2008"/> An effective estimate of folding free energy change upon mutation is:
 
:<math>\Delta\Delta G_\text{fold} \approx E_\text{folded}(s') - E_\text{folded}(s) - \bigl[E_\text{unfolded}(s') - E_\text{unfolded}(s)\bigr]</math>
 
where <math>s</math> and <math>s'</math> are the wild-type and mutant sequences respectively.


Once all energy tables for a given backbone were returned from volunteers and assembled, a heuristic search algorithm rapidly explored the full sequence and conformational space, generating between 200,000 and 300,000 candidate sequences per backbone template and retaining the lowest-energy ones.<ref name="plosone2010"/>
where <math>E_i</math> is the self-energy of the side chain at position <math>i</math> and <math>E_{ij}</math> is the pairwise interaction energy between positions <math>i</math> and <math>j</math>. This additive structure meant the expensive pairwise terms could be precomputed once and distributed across volunteer machines, making the calculation tractable at scale.<ref name="plos" /> 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 [[wikipedia:Protein structure prediction|protein structure prediction]], the study of protein evolution, and the design of new proteins.<ref name="wp" />


=== The BOINC infrastructure ===
[[File:Protein-structure.png|thumb|left|A protein's three-dimensional fold is compatible with a limited set of amino acid sequences, the "inverse folding" relationship proteins@home was built to explore]]


The project leveraged BOINC's client-server model. The Proteins@home server distributed work units (protein backbone files plus parameter inputs) to volunteers, who ran the energy table precomputation using idle CPU time. Completed energy tables were validated by quorum (comparing results from multiple independent hosts) before being accepted and assembled into the central database.<ref name="jcc2008"/> The project was listed among BOINC's official project directory at the URL <code>http://biology.polytechnique.fr/proteinsathome</code>.<ref name="boinc-oldprojects">{{cite web |url=https://github.com/BOINC/boinc-site/blob/master/old_projects.inc |title=old_projects.inc |publisher=GitHub / BOINC |access-date=2026-06-08}}</ref>
== 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.


=== Comparison with related BOINC protein projects ===
{{#ev:youtube|aM6kiaM228Y|700|center|proteins@home BOINC screensaver|start=0}}


Proteins@home was one of several BOINC-based projects focused on protein science active in the mid-2000s. [[Rosetta@home]], operated by the Baker Lab at the University of Washington, focused on forward structure prediction and protein-protein docking, and is still active. [[Predictor@home]], based at the Burnham Institute, was the first independent BOINC project ever launched and entered predictions in the [[CASP]] biennial evaluation of protein structure prediction methods.<ref>{{cite encyclopedia |title=Predictor@home |encyclopedia=Wikipedia |url=https://en.wikipedia.org/wiki/Predictor@home |access-date=2026-06-08}}</ref> [[POEM@Home]], hosted at the Karlsruhe Institute of Technology, modelled protein folding dynamics using [[Anfinsen's dogma]] and ran from 2007 to 2016.<ref>{{cite encyclopedia |title=POEM@Home |encyclopedia=Wikipedia |url=https://en.wikipedia.org/wiki/POEM@Home |access-date=2026-06-08}}</ref>
== 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.<ref name="wayback" /> 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.<ref name="jcc" />


What distinguished Proteins@home from these projects was its focus on the ''inverse'' problem — designing sequences to fit given folds — rather than predicting folds from sequences. It also aimed to cover a large, systematic slice of protein fold space (roughly 1,500 folds) rather than working on individual targets or a specific set of challenge proteins.
== Publications ==
 
The following papers are listed on [https://boinc.berkeley.edu/pubs.php#Proteins@home the official BOINC publications page] as scientific results arising from HashClash's BOINC-based computing.
== Scientific publications ==
* Schmidt am Busch, Marcel, Audrey Sedano and Thomas Simonson. [https://dx.plos.org/10.1371/journal.pone.0010410 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. [https://onlinelibrary.wiley.com/doi/10.1002/prot.22426 Computational protein design as a tool for fold recognition]. Proteins: Structure, Function, and Bioinformatics (2009). DOI: 10.1002/prot.22426.
[[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>]]
* Schmidt Am Busch, Marcel, Anne Lopes, David Mignon and Thomas Simonson. [https://onlinelibrary.wiley.com/doi/10.1002/jcc.20870 Computational protein design: Software implementation, parameter optimization, and performance of a simple model]. Journal of Computational Chemistry (2008). DOI: 10.1002/jcc.20870.<ref name="jcc">{{Cite journal |last1=Schmidt Am Busch |first1=Marcel |last2=Lopes |first2=Anne |last3=Mignon |first3=David |last4=Simonson |first4=Thomas |title=Computational protein design: Software implementation, parameter optimization, and performance of a simple model |journal=Journal of Computational Chemistry |volume=29 |issue=7 |pages=1092–1102 |date=2008-05-29 |doi=10.1002/jcc.20870 |pmid=18069664 |url=https://onlinelibrary.wiley.com/doi/10.1002/jcc.20870}}</ref>
 
* am Busch, Marcel Schmidt, Anne Lopes, Najette Amara, Christine Bathelt and Thomas Simonson. [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-148 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.
The Proteins@home computing platform directly enabled several peer-reviewed publications from the Simonson group.
* Schmidt am Busch, Marcel, Anne Lopes, David Mignon, Thomas Gaillard and Thomas Simonson. [https://doi.org/10.1007/978-94-007-4948-1_7 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.
 
=== Computational protein design: software and benchmarks (2008) ===
 
The primary methods paper describing the Proteins@home software pipeline, parameter optimisation, and performance on a simple molecular mechanics model was published in the ''Journal of Computational Chemistry'' in 2008.<ref name="jcc2008"/> The paper validated the approach against experimental data and described the BOINC-distributed workflow in detail.
 
=== Testing the Coulomb/ASA solvent model (2008) ===
 
A companion study in ''BMC Bioinformatics'' used the Proteins@home platform to evaluate the Coulomb/accessible-surface-area implicit solvent model for protein stability, ligand binding free energies, and protein design.<ref name="bmc2008"/> The calculations were performed using volunteer computers in over 70 countries. The model was benchmarked against experimental mutation free energies and binding affinities across a range of proteins and peptides.
 
=== Fold recognition via computational design (2010) ===
 
A follow-up study published in ''PLOS ONE'' after the project's conclusion used the Proteins@home-generated sequence libraries to investigate whether computationally designed sequences could supplement natural sequences for protein fold recognition and homology searching.<ref name="plosone2010"/> Four [[SCOP]] families were redesigned — Small Kunitz-type inhibitors, Interleukin-8 chemokines, PDZ domains, and Caspase catalytic subunits — across 43 backbone templates. The SUPERFAMILY profile Hidden Markov Model library recognised 85% of the low-energy designed sequences as native-like, supporting the utility of designed sequences as diverse complements to experimental databases.
 
== Legacy and successor work ==
 
Although the volunteer computing phase of the project ran for only about 18 months, its distributed energy table calculations made possible a systematic exploration of protein sequence space at a scale that would not have been feasible on the group's local hardware alone.
 
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>


== See also ==
== See also ==
 
* [[SIMAP]]
* [[BOINC]]
* [[wikipedia:BOINC|BOINC]]
* [[Rosetta@home]]
* [[wikipedia:Protein design|Protein design]]
* [[Predictor@home]]
* [[wikipedia:Protein structure prediction|Protein structure prediction]]
* [[POEM@Home]]
* [[wikipedia:Volunteer computing|Volunteer computing]]
* [[Protein structure prediction]]
* [[Computational protein design]]
* [[Folding@home]]
* [[École Polytechnique]]


== References ==
== References ==
{{Reflist}}
{{Reflist}}


== External links ==
* [https://web.archive.org/web/20080101000000*/http://biology.polytechnique.fr/proteinsathome/ Proteins@home official website (Wayback Machine)]
* [https://proteus.polytechnique.fr/ Proteus]  successor software package, École Polytechnique
* [https://commons.wikimedia.org/wiki/Category:Proteins@home Proteins@home] at Wikimedia Commons
* [https://boinc.berkeley.edu/pubs.php Publications by BOINC Projects] at boinc.berkeley.edu
[[Category:BOINC projects]]
[[Category:Completed BOINC projects]]
[[Category:Completed BOINC projects]]
[[Category:Biochemistry]]
[[Category:Biochemistry]]
[[Category:Computational biology]]
[[Category:Volunteer computing projects]]
[[Category:Protein structure]]
[[Category:École Polytechnique]]
[[Category:Science and technology in France]]
[[Category:2006 establishments in France]]
[[Category:2008 disestablishments]]

Latest revision as of 14:10, 5 July 2026








proteins@home
The proteins@home screensaver
Project
StatusCompleted
CategoryBiochemistry
ComputeCPU
RequiresNone
Development
DeveloperDepartment of Biology, École Polytechnique
AuthorThomas Simonson
SponsorÉcole Polytechnique
MaintainerMarcel Schmidt am Busch
Initial releaseDecember 28, 2006  (20 years ago)
CompletedJune 2008
Software
Operating systemWindows, Linux, macOS
Metadata
Websitehttp://biology.polytechnique.fr/proteinsathome/ (archived)


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]

The École Polytechnique campus in Palaiseau, France, where proteins@home was based

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 σ could be decomposed as

E(σ)=∑iEi(σi)+∑i<jEij(σi,σj)

where Ei is the self-energy of the side chain at position i and Eij is the pairwise interaction energy between positions i and j. 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]

A protein's three-dimensional fold is compatible with a limited set of amino acid sequences, the "inverse folding" relationship proteins@home was built to explore

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.

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proteins@home BOINC screensaver

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.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 proteins@home. Wikipedia. Retrieved 2026-07-05.
  2. ↑ BOINC project news archive. BOINC-site GitHub repository. BOINC. Retrieved 2026-07-05.
  3. ↑ 3.0 3.1 proteins@home. Wayback Machine. Retrieved 2026-07-05.
  4. ↑ Proteins@Home. BOINC wiki. University of California, Berkeley. Retrieved 2026-07-05.
  5. ↑ 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.
  6. ↑ https://boinc.berkeley.edu/forum_thread.php?id=5136
  7. ↑ (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.
  8. ↑ The Proteus software for computational protein design. École Polytechnique. Retrieved 2026-06-08.
  9. ↑ boinc_news.php (BOINC site source). GitHub / BOINC. Retrieved 2026-06-08.
  10. ↑ (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. ↑ 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.
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