POEM@HOME - Revision history

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2026-07-18T19:24:04Z

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	'''POEM@HOME''' (also written '''POEM@Home''') was a [[wikipedia:volunteer computing\|volunteer computing]] project running on the [[wikipedia:Berkeley Open Infrastructure for Network Computing\|Berkeley Open Infrastructure for Network Computing (BOINC)]] platform.<ref name="wp-newsarchive">{{Cite web \|url=http://boinc.fzk.de/poem/old_news.php \|title=News archive \|website=boinc.fzk.de \|publisher=Karlsruhe Institute of Technology \|archive-url=https://web.archive.org/web/20140224005936/http://boinc.fzk.de/poem/old_news.php \|archive-date=2014-02-24 \|url-status=dead \|access-date=2026-07-18}}</ref><ref name="end-announcement">{{Cite web \|url=http://boinc.fzk.de/poem/forum_thread.php?id=1280 \|title=The Future of POEM@HOME \|website=boinc.fzk.de \|publisher=Karlsruhe Institute of Technology \|date=2016-10-04 \|archive-url=https://web.archive.org/web/20161009200537/http://boinc.fzk.de/poem/forum_thread.php?id=1280 \|archive-date=2016-10-09 \|url-status=dead \|access-date=2026-07-18}}</ref> The project was hosted by the [[wikipedia:Karlsruhe Institute of Technology\|Karlsruhe Institute of Technology (KIT)]], specifically the Institute of Nanotechnology (INT), in the research group of Prof. Dr. Wolfgang Wenzel.<ref name="strunk-bio">{{Cite web \|url=http://www.timo-strunk.de/?page_id=4 \|title=About Me \|website=timo-strunk.de \|author=Strunk, Timo \|access-date=2026-07-18}}</ref> POEM@HOME used [[wikipedia:volunteer computing\|volunteers']] idle computer time to simulate [[wikipedia:protein folding\|protein folding]] and predict [[wikipedia:protein structure prediction\|protein structure]] from [[wikipedia:amino acid\|amino acid]] sequence, based on [[wikipedia:Anfinsen's dogma\|Anfinsen's dogma]], the hypothesis that a protein's biologically active, native conformation corresponds to the global minimum of its [[wikipedia:Gibbs free energy\|free energy]] landscape.<ref name="wp-newsarchive" /><ref name="verma-pff02">{{Cite journal \|authors=Verma, A., Wenzel, W. \|title=A Free-Energy Approach for All-Atom Protein Simulation \|journal=Biophysical Journal \|volume=96 \|issue=9 \|pages=3483-3494 \|date=2009 \|doi=10.1016/j.bpj.2008.12.3921}}</ref> The project ran from 2007 until it was formally retired in October 2016, after advances in GPU-accelerated simulation reduced its need for volunteered CPU time.<ref name="wp-newsarchive" /><ref name="end-announcement" />		'''[https://web.archive.org/http://boinc.fzk.de/poem/ POEM@HOME]''' (also written '''POEM@Home''') was a [[wikipedia:volunteer computing\|volunteer computing]] project running on the [[wikipedia:Berkeley Open Infrastructure for Network Computing\|Berkeley Open Infrastructure for Network Computing (BOINC)]] platform.<ref name="wp-newsarchive">{{Cite web \|url=http://boinc.fzk.de/poem/old_news.php \|title=News archive \|website=boinc.fzk.de \|publisher=Karlsruhe Institute of Technology \|archive-url=https://web.archive.org/web/20140224005936/http://boinc.fzk.de/poem/old_news.php \|archive-date=2014-02-24 \|url-status=dead \|access-date=2026-07-18}}</ref><ref name="end-announcement">{{Cite web \|url=http://boinc.fzk.de/poem/forum_thread.php?id=1280 \|title=The Future of POEM@HOME \|website=boinc.fzk.de \|publisher=Karlsruhe Institute of Technology \|date=2016-10-04 \|archive-url=https://web.archive.org/web/20161009200537/http://boinc.fzk.de/poem/forum_thread.php?id=1280 \|archive-date=2016-10-09 \|url-status=dead \|access-date=2026-07-18}}</ref> The project was hosted by the [[wikipedia:Karlsruhe Institute of Technology\|Karlsruhe Institute of Technology (KIT)]], specifically the Institute of Nanotechnology (INT), in the research group of Prof. Dr. Wolfgang Wenzel.<ref name="strunk-bio">{{Cite web \|url=http://www.timo-strunk.de/?page_id=4 \|title=About Me \|website=timo-strunk.de \|author=Strunk, Timo \|access-date=2026-07-18}}</ref> POEM@HOME used [[wikipedia:volunteer computing\|volunteers']] idle computer time to simulate [[wikipedia:protein folding\|protein folding]] and predict [[wikipedia:protein structure prediction\|protein structure]] from [[wikipedia:amino acid\|amino acid]] sequence, based on [[wikipedia:Anfinsen's dogma\|Anfinsen's dogma]], the hypothesis that a protein's biologically active, native conformation corresponds to the global minimum of its [[wikipedia:Gibbs free energy\|free energy]] landscape.<ref name="wp-newsarchive" /><ref name="verma-pff02">{{Cite journal \|authors=Verma, A., Wenzel, W. \|title=A Free-Energy Approach for All-Atom Protein Simulation \|journal=Biophysical Journal \|volume=96 \|issue=9 \|pages=3483-3494 \|date=2009 \|doi=10.1016/j.bpj.2008.12.3921}}</ref> The project ran from 2007 until it was formally retired in October 2016, after advances in GPU-accelerated simulation reduced its need for volunteered CPU time.<ref name="wp-newsarchive" /><ref name="end-announcement" />

	The POEM@HOME client applications were proprietary and were not released as open-source software.<ref name="wp-newsarchive" />		The POEM@HOME client applications were proprietary and were not released as open-source software.<ref name="wp-newsarchive" />

Al Piskun: first light

2026-07-18T19:23:10Z

first light

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{{Infobox software
| name = POEM@HOME
| logo =POEM@HOME.jpg
| logo caption =POEM@HOME logo
| screenshot =
| caption =
| description = POEM@HOME was a completed BOINC volunteer computing project hosted by the Karlsruhe Institute of Technology that used all-atom free-energy simulations to predict protein structure and folding, running from 2007 to 2016.
| status = Completed
| category = Biochemistry
| compute = CPU & GPU
| dependencies = None
| developer = Institute of Nanotechnology (INT), Karlsruhe Institute of Technology
| author = Timo Strunk
| sponsor =
| maintainer = POEM@HOME team (Wenzel Group, INT, KIT)
| released = {{Start date and age|2007}}
| completed = {{Start date and age|2016|10|04}}
| discontinued =
| repository =
| programming language =
| operating system = Windows, Linux
| 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://boinc.fzk.de/poem/}} (defunct)
| license = Proprietary
}}

'''POEM@HOME''' (also written '''POEM@Home''') was a [[wikipedia:volunteer computing|volunteer computing]] project running on the [[wikipedia:Berkeley Open Infrastructure for Network Computing|Berkeley Open Infrastructure for Network Computing (BOINC)]] platform.<ref name="wp-newsarchive">{{Cite web |url=http://boinc.fzk.de/poem/old_news.php |title=News archive |website=boinc.fzk.de |publisher=Karlsruhe Institute of Technology |archive-url=https://web.archive.org/web/20140224005936/http://boinc.fzk.de/poem/old_news.php |archive-date=2014-02-24 |url-status=dead |access-date=2026-07-18}}</ref><ref name="end-announcement">{{Cite web |url=http://boinc.fzk.de/poem/forum_thread.php?id=1280 |title=The Future of POEM@HOME |website=boinc.fzk.de |publisher=Karlsruhe Institute of Technology |date=2016-10-04 |archive-url=https://web.archive.org/web/20161009200537/http://boinc.fzk.de/poem/forum_thread.php?id=1280 |archive-date=2016-10-09 |url-status=dead |access-date=2026-07-18}}</ref> The project was hosted by the [[wikipedia:Karlsruhe Institute of Technology|Karlsruhe Institute of Technology (KIT)]], specifically the Institute of Nanotechnology (INT), in the research group of Prof. Dr. Wolfgang Wenzel.<ref name="strunk-bio">{{Cite web |url=http://www.timo-strunk.de/?page_id=4 |title=About Me |website=timo-strunk.de |author=Strunk, Timo |access-date=2026-07-18}}</ref> POEM@HOME used [[wikipedia:volunteer computing|volunteers']] idle computer time to simulate [[wikipedia:protein folding|protein folding]] and predict [[wikipedia:protein structure prediction|protein structure]] from [[wikipedia:amino acid|amino acid]] sequence, based on [[wikipedia:Anfinsen's dogma|Anfinsen's dogma]], the hypothesis that a protein's biologically active, native conformation corresponds to the global minimum of its [[wikipedia:Gibbs free energy|free energy]] landscape.<ref name="wp-newsarchive" /><ref name="verma-pff02">{{Cite journal |authors=Verma, A., Wenzel, W. |title=A Free-Energy Approach for All-Atom Protein Simulation |journal=Biophysical Journal |volume=96 |issue=9 |pages=3483-3494 |date=2009 |doi=10.1016/j.bpj.2008.12.3921}}</ref> The project ran from 2007 until it was formally retired in October 2016, after advances in GPU-accelerated simulation reduced its need for volunteered CPU time.<ref name="wp-newsarchive" /><ref name="end-announcement" />

The POEM@HOME client applications were proprietary and were not released as open-source software.<ref name="wp-newsarchive" />

[[File:Karlsruhe Uni Hauptgebaeude.jpg|thumb|The main building of the Karlsruhe Institute of Technology, the project's host institution]]

== Overview ==

POEM@HOME investigated how [[wikipedia:protein structure|protein structure]] determines protein function, attempted to predict a protein's three-dimensional structure directly from its amino acid sequence, studied how [[wikipedia:protein-protein interaction|proteins interact]] with one another, and examined how malfunctioning proteins can give rise to functional disorders, with the eventual goal of supporting the development of medical treatments.<ref name="wp-newsarchive" /> The BOINC server component of POEM@HOME was developed by Timo Strunk as part of his diploma thesis in the Wenzel group, building on an existing Monte Carlo simulation package known as ''jpoem''.<ref name="strunk-bio" />

== Scientific approach ==

The scientific core of POEM@HOME was an all-atom [[wikipedia:force field (chemistry)|free-energy force field]], developed over several years by the Wenzel group and referred to in successive versions as PFF01 and PFF02.<ref name="verma-pff02" /> Rather than simulating the physical, time-resolved dynamics of folding as [[wikipedia:molecular dynamics|molecular dynamics]] methods do, the force field approach evaluated a free-energy function for a very large number of candidate conformations and searched for the conformation of lowest free energy using stochastic optimization techniques such as basin-hopping and evolutionary algorithms.<ref name="verma-pff02" /> This is the computational expression of Anfinsen's dogma: the predicted native structure <math>x^*</math> is the conformation that minimizes the free energy function <math>E(x)</math> over the space of possible conformations,

<math>x^* = \arg\min_{x} E(x)</math>

where the free-energy function itself was built up from several physical contributions, schematically

<math>E(x) = E_{\text{LJ}}(x) + E_{\text{elec}}(x) + E_{\text{HB}}(x) + E_{\text{solv}}(x)</math>

combining a [[wikipedia:Lennard-Jones potential|Lennard-Jones]] term, an atomically resolved electrostatic term, a hydrogen-bonding term, and an implicit solvation term based on solvent-accessible surface area.<ref name="verma-pff02" /> Distributing this exhaustive conformational search across thousands of volunteered computers was the central reason the project was built on BOINC.<ref name="strunk-simona">{{Cite journal |authors=Strunk, T., Wolf, M., Brieg, M., Klenin, K., Biewer, A., Tristram, F., Ernst, M., Kleine, P. J., Heilmann, N., Kondov, I., Wenzel, W. |title=SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems |journal=Journal of Computational Chemistry |volume=33 |issue=32 |pages=2602-2613 |date=2012 |doi=10.1002/jcc.23089 |url=https://onlinelibrary.wiley.com/doi/10.1002/jcc.23089}}</ref>

[[File:Protein structure (1).png|thumb|Illustration of a folded protein tertiary structure, the kind of conformation POEM@HOME attempted to predict from sequence]]

== Software framework ==

In its later years the project's simulations were run on '''SIMONA''' (SImulation of MOlecular and NAnoscale systems), a generic Monte Carlo based simulation framework developed at the Institute of Nanotechnology, KIT, and described in a 2012 paper by Strunk, Wolf, Brieg, Klenin and colleagues.<ref name="strunk-simona" /> SIMONA was built to be usable through a graphical interface for standard runs while also being parallelized across [[wikipedia:Message Passing Interface|MPI]] and [[wikipedia:graphics processing unit|GPU]] resources, and was applied not only to protein conformational sampling but also to protein-protein association, small-molecule protein docking, and simulation of nanoscale organic molecule clusters.<ref name="strunk-simona" /><ref name="simona-int">{{Cite web |url=https://www.int.kit.edu/1636.php |title=SIMONA (SImulation of MOlecular and NAnoscale systems) |website=int.kit.edu |publisher=Institute of Nanotechnology, Karlsruhe Institute of Technology |access-date=2026-07-18}}</ref> A GPU-optimized version of SIMONA was completed in 2015, which the project team reported sped up calculations "by various magnitudes" compared to the CPU-only workflow that BOINC volunteers had been supporting.<ref name="end-announcement" /> Around the same period the project also released [[wikipedia:OpenCL|OpenCL]]-based GPU applications for AMD/ATI hardware, distributing separate CPU workunits (branded "firstdrug") and GPU workunits (branded "gpucrystal") aimed at drug-development calculations.<ref name="bcteam-forum">{{Cite web |url=https://www.bc-team.org/viewtopic.php?f=23&t=321 |title=POEM@home |website=bc-team.org |publisher=BOINC Confederation |access-date=2026-07-18}}</ref>

== Participation in CASP ==

POEM@HOME took part in [[wikipedia:CASP|CASP]] (Critical Assessment of Techniques for Protein Structure Prediction), including CASP8 in 2008, submitting predictions generated with volunteer-computed workunits.<ref name="bcteam-forum" /> According to the project team's own retrospective, the CASP experience showed that POEM's forcefield-based approach was particularly effective at ''quality assessment'', that is, the biophysical evaluation and ranking of candidate protein structures, rather than at generating entirely new folds from scratch (''de novo'' modelling).<ref name="bcteam-forum" />

== Applications and outcomes ==

The project team reported using POEM@HOME's methods to help identify a gene associated with a rare, late-stage developmental disorder said to affect roughly 1 in 10,000 births, an outcome the team highlighted in project communications as a direct application of the project's computational biology work to human disease.<ref name="bcteam-forum" /> The project's underlying force-field and simulation methods were also applied by the Wenzel group and collaborators to problems including protein-protein interface analysis, small-peptide receptor binding, and protein engineering, several examples of which are listed in [[#Publications|Publications]] below.

== History ==

POEM@HOME began operating in 2007.<ref name="wp-newsarchive" /> Over the following years its BOINC volunteer base contributed CPU time toward the group's protein folding and structure-prediction studies, including the CASP8 competition in 2008.<ref name="bcteam-forum" /> Following the development of a GPU-accelerated version of the SIMONA simulation framework in 2015, the project's in-house computational capacity grew so large that it "did not require [volunteers'] large and generous contributions" to continue its science.<ref name="end-announcement" /> On 4 October 2016, the project team posted "The Future of POEM@HOME," thanking contributors and announcing the project's retirement after eight years of operation, while encouraging volunteers to redirect their computing time to other, smaller BOINC projects with greater need.<ref name="end-announcement" /> The project's closure was independently noted by BOINC volunteers on other project forums shortly afterward.<ref name="foldingforum">{{Cite web |url=https://foldingforum.org/viewtopic.php?p=289540 |title=Can Folding@home be added as a BOINC project? |website=foldingforum.org |date=2016-10-17 |access-date=2026-07-18}}</ref>

== See also ==

* [[Predictor@home]]
* [[wikipedia:BOINC|BOINC]]
* [[wikipedia:Protein structure prediction|Protein structure prediction]]
* [[wikipedia:CASP|CASP]]

== Publications ==

This is a list papers containing scientific results arising, directly or indirectly, from BOINC-based computing. See https://boinc.berkeley.edu/pubs.php#POEM@HOME
# {{Cite journal |authors=Strunk, T., Wolf, M., Wenzel, W. |title=Peptide structure prediction using distributed volunteer computing networks |journal=Journal of Mathematical Chemistry |date=2012 |doi=10.1007/s10910-011-9937-x |url=http://link.springer.com/10.1007/s10910-011-9937-x}}
# {{Cite journal |authors=Strunk, T., Wolf, M., Brieg, M., Klenin, K., Biewer, A., Tristram, F., Ernst, M., Kleine, P. J., Heilmann, N., Kondov, I., Wenzel, W. |title=SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems |journal=Journal of Computational Chemistry |volume=33 |issue=32 |pages=2602-2613 |date=2012 |doi=10.1002/jcc.23089 |url=https://onlinelibrary.wiley.com/doi/10.1002/jcc.23089}}
# {{Cite journal |authors=Meliciani, I., Klenin, K., Strunk, T., Schmitz, K., Wenzel, W. |title=Probing hot spots on protein-protein interfaces with all-atom free-energy simulation |journal=The Journal of Chemical Physics |date=2009 |doi=10.1063/1.3177008 |url=http://aip.scitation.org/doi/10.1063/1.3177008}}
# {{Cite journal |authors=Girrbach, M., Meliciani, I., Waterkotte, B. et al. |title=A fluorescence polarization assay for the experimental validation of an in silico model of the chemokine CXCL8 binding to receptor-derived peptides |journal=Physical Chemistry Chemical Physics |date=2014 |doi=10.1039/C3CP53850H |url=https://pubs.rsc.org/en/content/articlelanding/2014/cp/c3cp53850h}}
# {{Cite journal |authors=Boeuf, S., Throm, T., Gutt, B. et al. |title=Engineering hydrophobin DewA to generate surfaces that enhance adhesion of human but not bacterial cells |journal=Acta Biomaterialia |date=2012 |doi=10.1016/j.actbio.2011.11.022 |url=https://linkinghub.elsevier.com/retrieve/pii/S1742706111005253}}

== References ==
{{Reflist}}

[[Category:Completed BOINC projects]]
[[Category:Biochemistry]]