Predictor@home - Revision history

Al Piskun: first light

2026-06-03T13:45:35Z

first light

← Older revision		Revision as of 13:45, 3 June 2026
Line 1:		Line 1:
	{{Infobox software		{{Infobox software
	\| name = Predictor@home		\| name = Predictor@home
	\| logo = Predictor.~~png~~		\| logo = Predictor.gif
	\| logo caption = Predictor@home project image		\| logo caption = Predictor@home project image
	\| screenshot =		\| screenshot =Predictor.png
	\| caption =		\| caption =
	\| description = Predictor@home was the first independent BOINC-based volunteer computing project, run by The Scripps Research Institute to predict protein tertiary structure from amino acid sequences, active from 2004 to 2009.		\| description = Predictor@home was the first independent BOINC-based volunteer computing project, run by The Scripps Research Institute to predict protein tertiary structure from amino acid sequences, active from 2004 to 2009.
Line 16:		Line 16:
	\| sponsor = The Scripps Research Institute		\| sponsor = The Scripps Research Institute
	\| maintainer = Michela Taufer		\| maintainer = Michela Taufer
	\| released = {{Start date and age\|2004\|06\|09}}		\| released = {{Start date and age\|2004\|05\|04}}
	\| completed =		\| completed =
	\| discontinued = {{Start date and age\|2009\|06\|10}}		\| discontinued = {{Start date and age\|2009\|06\|10}}
Line 37:		Line 37:
	\| cpu performance =		\| cpu performance =

	\| website = {{URL\|~~https://web.archive.org/web/20081128162813/~~http://predictor.chem.lsa.umich.edu/}}		\| website = {{URL\|http://predictor.chem.lsa.umich.edu/}}
	\| license =		\| license =
	}}		}}

	'''Predictor@home''' (also known as '''ProteinPredictorAtHome''' or '''P@H''') was a [[volunteer computing]] project that used the [[Berkeley Open Infrastructure for Network Computing]] (BOINC) framework to predict [[protein structure prediction\|protein tertiary structure]] from amino acid sequences. It was developed and run by [[Michela Taufer]] and [[Charles L. Brooks III]] at [[Scripps Research\|The Scripps Research Institute]] in La Jolla, California.<ref name="taufer2005global">Taufer, M., An, C., Kerstens, A., Brooks III, C.L. (2005). "Predictor@Home: A 'Protein Structure Prediction Supercomputer' Based on Global Computing". ''IEEE Transactions on Parallel and Distributed Systems''. {{doi\|10.1109/TPDS.2006.148}}</ref> The project holds the notable distinction of being the '''first independent BOINC-based project''' ever launched, going live on '''9 June 2004'''.<ref name="boinchistory">Marc Seil (17 January 2007). [https://isaac.ssl.berkeley.edu/forum_thread.php?id=1456 "BOINC History"]. BOINC message boards. Retrieved 2022-11-05.</ref><ref name="wikidata">{{cite web \|url=https://www.wikidata.org/wiki/Q902260 \|title=Predictor@home \|publisher=Wikidata \|access-date=2024-01-01}}</ref>		'''[https://web.archive.org/web/20081128162813/http://predictor.chem.lsa.umich.edu/ Predictor@home]''' (also known as '''ProteinPredictorAtHome''' or '''P@H''') was a [[volunteer computing]] project that used the [[Berkeley Open Infrastructure for Network Computing]] (BOINC) framework to predict [[protein structure prediction\|protein tertiary structure]] from amino acid sequences. It was developed and run by [[Michela Taufer]] and [[Charles L. Brooks III]] at [[Scripps Research\|The Scripps Research Institute]] in La Jolla, California.<ref name="taufer2005global">Taufer, M., An, C., Kerstens, A., Brooks III, C.L. (2005). "Predictor@Home: A 'Protein Structure Prediction Supercomputer' Based on Global Computing". ''IEEE Transactions on Parallel and Distributed Systems''. {{doi\|10.1109/TPDS.2006.148}}</ref> The project holds the notable distinction of being the '''first independent BOINC-based project''' ever launched, going live on '''9 June 2004'''.<ref name="boinchistory">Marc Seil (17 January 2007). [https://isaac.ssl.berkeley.edu/forum_thread.php?id=1456 "BOINC History"]. BOINC message boards. Retrieved 2022-11-05.</ref><ref name="wikidata">{{cite web \|url=https://www.wikidata.org/wiki/Q902260 \|title=Predictor@home \|publisher=Wikidata \|access-date=2024-01-01}}</ref>

	~~[[File:Predictor.png\|thumb\|right\|250px\|Predictor@home visualisation of a protein structure prediction run.]]~~

	== Background ==		== Background ==
Line 68:		Line 66:

	Predictor@home was deployed specifically to compete in CASP6 and to test whether volunteer computing could deliver meaningful improvements over traditional cluster computing for protein structure prediction. During this period, the project attracted '''6,786 users''' and accumulated over '''12 billion seconds''' of total compute time.<ref name="taufer2005global" />		Predictor@home was deployed specifically to compete in CASP6 and to test whether volunteer computing could deliver meaningful improvements over traditional cluster computing for protein structure prediction. During this period, the project attracted '''6,786 users''' and accumulated over '''12 billion seconds''' of total compute time.<ref name="taufer2005global" />

	~~[[File:Scripps Research Institute.jpg\|thumb\|right\|220px\|The Scripps Research Institute in La Jolla, California, where Predictor@home was developed.]]~~

	The project significantly increased sampling capacity by '''one to two orders of magnitude''' compared to what was achievable with a local computer cluster, greatly improving the chances of finding near-native protein conformations. For 81% of the CASP6 target proteins, Predictor@home achieved more than 3,000 independent structure samples; for 48% of targets, it exceeded 10,000 samples.<ref name="taufer2005global" />		The project significantly increased sampling capacity by '''one to two orders of magnitude''' compared to what was achievable with a local computer cluster, greatly improving the chances of finding near-native protein conformations. For 81% of the CASP6 target proteins, Predictor@home achieved more than 3,000 independent structure samples; for 48% of targets, it exceeded 10,000 samples.<ref name="taufer2005global" />
Line 76:		Line 72:

	During the peak of the CASP6 period, the server infrastructure could not keep pace with the rapid growth in participants, and user account creation was temporarily suspended to manage server load.<ref name="taufer2005pub" />		During the peak of the CASP6 period, the server infrastructure could not keep pace with the rapid growth in participants, and user account creation was temporarily suspended to manage server load.<ref name="taufer2005pub" />
			[[File:Scripps Florida Building B.JPG\|thumb\|340x340px\|The Scripps Research Institute in La Jolla, California, where Predictor@home was developed.]]

	=== Later Development and Shutdown ===		=== Later Development and Shutdown ===
Line 92:		Line 89:

	The task assigned to each volunteer computer was to generate independent samples of protein conformations for a given target sequence and return the resulting structures to the central server. Because each work unit was independent, the sampling was [[embarrassingly parallel]], making volunteer computing an ideal fit.		The task assigned to each volunteer computer was to generate independent samples of protein conformations for a given target sequence and return the resulting structures to the central server. Because each work unit was independent, the sampling was [[embarrassingly parallel]], making volunteer computing an ideal fit.

			[[File:Predictor.png\|thumb\|340x340px\|Predictor@home visualisation of a protein structure prediction run.]]

	=== Homogeneous Redundancy ===		=== Homogeneous Redundancy ===

Al Piskun: first light

2026-06-03T13:31:13Z

first light

New page

{{Infobox software
| name = Predictor@home
| logo = Predictor.png
| logo caption = Predictor@home project image
| screenshot =
| caption =
| description = Predictor@home was the first independent BOINC-based volunteer computing project, run by The Scripps Research Institute to predict protein tertiary structure from amino acid sequences, active from 2004 to 2009.

| status = Completed
| category = Biology and Medicine
| compute = CPU
| dependencies = None

| developer = Michela Taufer, C.L. Brooks III
| author = Michela Taufer
| sponsor = The Scripps Research Institute
| maintainer = Michela Taufer
| released = {{Start date and age|2004|06|09}}
| completed =
| discontinued = {{Start date and age|2009|06|10}}
| repository =

| programming language = C, C++
| operating system = Windows, Linux, macOS (x86)
| size =

| stats as of =
| average performance =
| active users =
| total users =
| active hosts =
| total hosts =

| rac =
| credit per day =
| gpu performance =
| cpu performance =

| website = {{URL|https://web.archive.org/web/20081128162813/http://predictor.chem.lsa.umich.edu/}}
| license =
}}

'''Predictor@home''' (also known as '''ProteinPredictorAtHome''' or '''P@H''') was a [[volunteer computing]] project that used the [[Berkeley Open Infrastructure for Network Computing]] (BOINC) framework to predict [[protein structure prediction|protein tertiary structure]] from amino acid sequences. It was developed and run by [[Michela Taufer]] and [[Charles L. Brooks III]] at [[Scripps Research|The Scripps Research Institute]] in La Jolla, California.<ref name="taufer2005global">Taufer, M., An, C., Kerstens, A., Brooks III, C.L. (2005). "Predictor@Home: A 'Protein Structure Prediction Supercomputer' Based on Global Computing". ''IEEE Transactions on Parallel and Distributed Systems''. {{doi|10.1109/TPDS.2006.148}}</ref> The project holds the notable distinction of being the '''first independent BOINC-based project''' ever launched, going live on '''9 June 2004'''.<ref name="boinchistory">Marc Seil (17 January 2007). [https://isaac.ssl.berkeley.edu/forum_thread.php?id=1456 "BOINC History"]. BOINC message boards. Retrieved 2022-11-05.</ref><ref name="wikidata">{{cite web |url=https://www.wikidata.org/wiki/Q902260 |title=Predictor@home |publisher=Wikidata |access-date=2024-01-01}}</ref>

[[File:Predictor.png|thumb|right|250px|Predictor@home visualisation of a protein structure prediction run.]]

== Background ==

[[Protein structure prediction]] is the challenge of determining the three-dimensional [[Protein tertiary structure|tertiary structure]] of a protein solely from its [[amino acid]] sequence. It is one of the most important problems in [[computational biology]], because a protein's structure governs its function, and knowing that structure can open the door to understanding diseases and designing new drugs.<ref name="taufer2005pub">Taufer, M., An, C., Kerstens, A., Brooks III, C.L. (2005). "Predictor@Home: A 'Protein Structure Prediction Supercomputer' Based on Public-Resource Computing". ''Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2005)''. {{doi|10.1109/IPDPS.2005.335}}</ref>

Experimental techniques such as [[X-ray crystallography]], [[nuclear magnetic resonance spectroscopy|NMR spectroscopy]], and [[cryogenic electron microscopy|cryo-EM]] can determine protein structures with high accuracy, but they are expensive and time-consuming. Computational methods can model protein structures much more quickly, but they require '''extensive sampling''' of the [[conformational space]] of possible protein shapes in order to find the most energetically stable native state. As the Predictor@home team described it:

{{blockquote|Predicting the structure of a protein from its amino acid sequence is a complex process the understanding of which could be used to gain new insight into the nature of protein function or provide targets for structure-based design of drugs to treat new and existing diseases.}}

For a protein with <math>n</math> residues, the number of possible backbone conformations grows exponentially, making exhaustive search computationally infeasible on any single machine. Predictor@home addressed this by distributing the sampling problem across thousands of volunteer computers worldwide.

The project was timed to align with the biannual '''[[CASP|Critical Assessment of Techniques for Protein Structure Prediction]]''' (CASP) competition, specifically the '''sixth round (CASP6)''' held in 2004. CASP is an international blind prediction challenge in which researchers predict the structures of proteins whose experimental structures have been determined but not yet published, providing a fair, independent benchmark of prediction methods.<ref name="casp6">{{cite web |url=https://predictioncenter.org/casp6/ |title=CASP6 |publisher=Prediction Center |access-date=2024-01-01}}</ref>

== History ==

=== Foundation and Launch ===

The BOINC framework was first released in April 2002 by [[David P. Anderson]] at the [[University of California, Berkeley]], initially developed to support [[SETI@home]].<ref name="anderson2004">Anderson, D.P. (2004). "BOINC: A System for Public-Resource Computing and Storage". ''5th IEEE/ACM International Workshop on Grid Computing'', pp. 365-372. {{doi|10.1109/GRID.2004.14}}</ref> Predictor@home became the '''first independent project''' to use BOINC outside of Berkeley, launching publicly on '''9 June 2004''' — two weeks before SETI@home's own BOINC-based relaunch on 22 June 2004.<ref name="boinchistory" /><ref name="wikidata" />

The project was set up and run by [[Michela Taufer]], then a postdoctoral fellow at The Scripps Research Institute and the University of California San Diego (UCSD), working alongside principal investigator [[Charles L. Brooks III]] in the Department of Molecular Biology.<ref name="taufer2005global" /><ref name="cra_taufer">{{cite web |url=https://cra.org/ccc/michela-taufer/ |title=Michela Taufer |publisher=Computing Research Association |access-date=2024-01-01}}</ref> The project URL was initially hosted at <code>predictor.scripps.edu</code>.

=== CASP6 Participation (2004) ===

Predictor@home was deployed specifically to compete in CASP6 and to test whether volunteer computing could deliver meaningful improvements over traditional cluster computing for protein structure prediction. During this period, the project attracted '''6,786 users''' and accumulated over '''12 billion seconds''' of total compute time.<ref name="taufer2005global" />

[[File:Scripps Research Institute.jpg|thumb|right|220px|The Scripps Research Institute in La Jolla, California, where Predictor@home was developed.]]

The project significantly increased sampling capacity by '''one to two orders of magnitude''' compared to what was achievable with a local computer cluster, greatly improving the chances of finding near-native protein conformations. For 81% of the CASP6 target proteins, Predictor@home achieved more than 3,000 independent structure samples; for 48% of targets, it exceeded 10,000 samples.<ref name="taufer2005global" />

Results showed that Predictor@home produced better predictions than a traditional local cluster for medium-difficulty and hard protein targets. However, very large "new fold" targets exceeding 300 residues proved more difficult, because the vast conformational space and limitations of the sampling algorithm made it hard to converge on good structures within the allotted time.<ref name="academia2005">{{cite web |url=https://www.academia.edu/3394630 |title=Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Global Computing |author=Taufer, M. et al. |year=2005 |access-date=2024-01-01}}</ref>

During the peak of the CASP6 period, the server infrastructure could not keep pace with the rapid growth in participants, and user account creation was temporarily suspended to manage server load.<ref name="taufer2005pub" />

=== Later Development and Shutdown ===

On '''6 September 2006''', Predictor@home was temporarily taken offline, with no new work units being distributed. In '''May 2008''', the project reverted to [[Software release life cycle#Alpha|alpha]] status while researchers experimented with new structural prediction methods. Over the summer of 2008, the project servers were migrated from Scripps to the [[University of Michigan]], with the new URL at <code>predictor.chem.lsa.umich.edu</code>.<ref name="macnn">{{cite web |url=https://web.archive.org/web/20111206170012/http://team.macnn.com/index.php?topic=predictor |title=Predictor has finished moving to Michigan |publisher=Team MacNN |date=2008-02-16 |access-date=2011-09-21}}</ref><ref name="umich">{{cite web |url=https://web.archive.org/web/20081108120407/http://predictor.chem.lsa.umich.edu/ |title=Predictor@Home (archived) |date=2008-11-08 |access-date=2022-11-05}}</ref>

By December 2008, the project had not sent out any work units for several months, and BOINC statistics sites were unable to obtain updated XML data, as this had been suspended by the project team. On '''10 June 2009''', the Predictor@home website and forums were shut down permanently.<ref name="enwp">{{cite web |url=https://en.wikipedia.org/wiki/Predictor@home |title=Predictor@home |publisher=Wikipedia |access-date=2024-01-01}}</ref>

== Science ==

=== The Protein Folding Problem ===

Proteins are [[polymer]]s made of chains of [[amino acids]]. In the cell, each newly synthesised protein spontaneously [[protein folding|folds]] into a specific three-dimensional shape that determines its biological function. The '''sequence-to-structure''' relationship is encoded in the [[energy landscape]] of the protein, and the native (functional) structure corresponds to a global free-energy minimum.

For a protein chain of <math>n</math> amino acid residues, each with backbone dihedral angles <math>\phi_i</math> and <math>\psi_i</math>, the number of possible conformations is astronomically large, illustrating why this is computationally hard. In practice, Predictor@home used [[physics]]-based all-atom [[force field (chemistry)|force fields]] with [[implicit solvation|implicit solvation models]] (the [[Generalized Born]] approximation) to score sampled conformations, combined with [[Monte Carlo simulation|Monte Carlo]] conformation sampling methods developed in the Brooks lab.<ref name="taufer2005pub" />

The task assigned to each volunteer computer was to generate independent samples of protein conformations for a given target sequence and return the resulting structures to the central server. Because each work unit was independent, the sampling was [[embarrassingly parallel]], making volunteer computing an ideal fit.

=== Homogeneous Redundancy ===

Because volunteer computers may run different hardware, different operating systems, and different software versions, and because participants can potentially tamper with results, data integrity is a significant concern for volunteer computing projects. Predictor@home addressed this through a technique called '''Homogeneous Redundancy''' (HR), which validates results by sending the same work unit to multiple volunteers and using strict equality comparisons to confirm that the returned results agree.<ref name="homredundancy">Taufer, M., Anderson, D.P., Cicotti, P., Brooks III, C.L. (2005). "Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing". ''Heterogeneous Computing Workshop, IPDPS 2005'', Denver.</ref> This ensured that floating-point computations performed across heterogeneous hardware produced consistent, trustworthy results.

=== GDT Score and Prediction Accuracy ===

CASP evaluates predictions using the '''Global Distance Test''' (GDT_TS) score, which measures the fraction of [[C-alpha]] atoms in a predicted model that can be superimposed onto the experimental structure within a given distance cutoff. A GDT_TS score of 100 would indicate a perfect prediction. For [[homology modeling]] and [[fold recognition]] targets, Predictor@home consistently matched or outperformed the best structures found on a local cluster, demonstrating the power of massive distributed sampling.<ref name="taufer2005global" />

== Comparison with Related Projects ==

Predictor@home was '''complementary''' to [[Folding@home]], the distributed computing project run by [[Vijay Pande]] at [[Stanford University]]. While Folding@home studies the ''dynamics'' of the protein folding process (how a protein transitions from an unfolded to a folded state over time), Predictor@home was focused on identifying the final [[tertiary structure]] — the endpoint itself — regardless of the pathway taken to get there.<ref name="enwp" /> The two projects also differed fundamentally in infrastructure: Predictor@home used the open BOINC platform, whereas Folding@home maintained its own entirely separate software stack.<ref name="enwp" />

Predictor@home also operated alongside [[Rosetta@home]], launched in 2005 by the [[David Baker (biochemist)|David Baker]] lab at the [[University of Washington]], which uses a different fragment-assembly approach (the [[Rosetta (software)|Rosetta]] algorithm) to predict protein structures. Each project represented a different computational philosophy for tackling the same underlying biological problem.<ref name="enwp" />

{| class="wikitable" style="width:100%; font-size:13px;"
|+ Comparison of protein structure prediction volunteer computing projects
! Project !! Institution !! BOINC? !! Approach !! Status
|-
| '''Predictor@home''' || Scripps Research / U. Michigan || Yes (first) || Physics-based Monte Carlo sampling || Completed (2009)
|-
| [[Rosetta@home]] || University of Washington || Yes || Fragment assembly (Rosetta) || Active
|-
| [[Folding@home]] || Stanford University || No (own platform) || Molecular dynamics of folding process || Active
|-
| [[proteins@home]] || Ecole Polytechnique || Yes || Large-scale non-profit prediction || Completed (2008)
|}

== Publications ==

The Predictor@home team produced several peer-reviewed publications describing the project's methods and results. Below is a selected bibliography.

# Taufer, M., An, C., Kerstens, A., Brooks III, C.L. (2006). "Predictor@Home: A 'Protein Structure Prediction Supercomputer' Based on Global Computing". ''IEEE Transactions on Parallel and Distributed Systems'' '''17'''(8): 786-796. {{doi|10.1109/TPDS.2006.148}}<ref name="taufer2005global" />
# Taufer, M., An, C., Kerstens, A., Brooks III, C.L. (2005). "Predictor@Home: A 'Protein Structure Prediction Supercomputer' Based on Public-Resource Computing". ''Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2005)''. {{doi|10.1109/IPDPS.2005.335}}<ref name="taufer2005pub" />
# Taufer, M., Anderson, D.P., Cicotti, P., Brooks III, C.L. (2005). "Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing". ''Heterogeneous Computing Workshop, IPDPS 2005'', Denver, April 4-8 2005.<ref name="homredundancy" />
# Estrada, T., Flores, D.A., Taufer, M., Teller, P.J., Kerstens, A., Anderson, D.P. (2006). "The Effectiveness of Threshold-Based Scheduling Policies in BOINC Projects". ''2006 Second IEEE International Conference on e-Science and Grid Computing''. {{doi|10.1109/E-SCIENCE.2006.261172}}
# Taufer, M., Kerstens, A., Estrada, T.P., Flores, D.A., Zamudio, R., Teller, P.J., Armen, R., Brooks, C.L. (2007). "Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling". ''2007 IEEE International Parallel and Distributed Processing Symposium''. {{doi|10.1109/IPDPS.2007.370668}}

== Legacy ==

Predictor@home left a lasting imprint on the history of distributed computing. As the first project to go live under the BOINC framework, it served as an early proof of concept that the BOINC platform could support independent scientific projects beyond SETI@home. Its techniques for managing result integrity (Homogeneous Redundancy) and for scheduling volunteer resources influenced later BOINC projects including [[Docking@home]], which was a successor project also run by Michela Taufer and applied the same infrastructure to [[protein-ligand docking]] problems in drug discovery.

The Predictor@home experience also informed subsequent work on BOINC performance simulation, leading to the development of '''EmBOINC''' and '''SimBA''' (Simulator of BOINC Applications), tools for predicting how BOINC projects will perform under varying volunteer conditions, which were published by the same research group.<ref name="simba">Taufer, M., Kerstens, A., Estrada, T., Flores, D., Teller, P.J. (2007). "SimBA: A Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects". ''21st International Workshop on Principles of Advanced and Distributed Simulation''. {{doi|10.1109/PADS.2007.27}}</ref>

== See also ==

* [[BOINC]]
* [[Rosetta@home]]
* [[Docking@home]]
* [[Michela Taufer]]

== References ==

{{Reflist}}

== External links ==

* [https://web.archive.org/web/20081128162813/http://predictor.chem.lsa.umich.edu/ Predictor@home (archived, University of Michigan mirror, November 2008)] via the Wayback Machine
* [https://en.wikipedia.org/wiki/Predictor@home Predictor@home] on Wikipedia
* [https://boinc.berkeley.edu/pubs.php Publications by BOINC Projects] - BOINC Berkeley
* [https://ieeexplore.ieee.org/document/1652942 Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Global Computing] on IEEE Xplore

[[Category:BOINC projects]]
[[Category:Completed BOINC projects]]
[[Category:Protein structure prediction]]
[[Category:Biology and Medicine]]
[[Category:Volunteer computing]]
[[Category:Distributed computing projects]]
[[Category:Scripps Research]]