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{{Infobox software
| name = TANPAKU
| logo =
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| description = TANPAKU was a Japanese BOINC volunteer computing project run by the Tokyo University of Science that used a Brownian dynamics method to study protein folding, operating from 2006 until a fatal server failure in 2008.
| status = Discontinued
| category = Structural biology
| compute = CPU
| dependencies =
| developer = Tadashi Ando, Ichiro Yamato (Yamato Laboratory); Takeda Laboratory
| author = Tadashi Ando
| sponsor = [[wikipedia:Tokyo University of Science|Tokyo University of Science]]
| maintainer =
| released = {{Start date and age|2005|08|02}}
| completed = No
| discontinued = {{Start date and age|2008|08|18}}
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| website = {{URL|http://issofty17.is.noda.tus.ac.jp/}}
| license =
}}

'''[https://web.archive.org/web/20060703095044/http://issofty17.is.noda.tus.ac.jp/index_E.php TANPAKU]''' was a Japanese [[BOINC]] [[wikipedia:volunteer computing|volunteer computing]] project dedicated to [[wikipedia:protein folding|protein folding]] and [[wikipedia:protein structure prediction|protein structure prediction]] research.<ref name="deWiki">{{Cite web |title=Tanpaku |url=https://de.wikipedia.org/wiki/Tanpaku |website=Wikipedia (German) |access-date=12 July 2026}}</ref> The project was based at the [[wikipedia:Tokyo University of Science|Tokyo University of Science]] and was jointly run by the Yamato Laboratory of the Department of Biological Science and Technology and the Takeda Laboratory of the Department of Information Sciences.<ref name="deWiki" /> Its name comes from the Japanese word ''tanpaku-shitsu'' ( 蛋白質 ), meaning "protein".<ref name="boincnews">{{Cite web |title=The TANPAKU project, based at the Tokyo University of Science, is open for participation |url=https://boinc.berkeley.edu/forum_thread.php?id=5103 |website=BOINC Message boards |date=7 July 2006 |access-date=12 July 2026}}</ref>

TANPAKU's first server message was on {{Start date and age|2005|08|02}} <ref>TANPAKU News Archive[https://web.archive.org/web/20060616191641/http://issofty17.is.noda.tus.ac.jp/old_news.php : https://web.archive.org/web/20060616191641/http://issofty17.is.noda.tus.ac.jp/old_news.php]</ref>and opened for public participation on {{Start date and age|2006|07|07}}, when BOINC founder [[wikipedia:David P. Anderson|David P. Anderson]] announced that the project studied "protein structure and function using a novel method called Brownian Dynamics".<ref name="boincnews" /> The project ran for roughly two years before a hardware failure took its server offline permanently, making it one of the shorter lived BOINC research projects.

== Overview ==
[[File:Tokyo University of Science Noda Campus.JPG|thumb|The Noda Campus of the Tokyo University of Science, home to the Yamato and Takeda laboratories that jointly ran TANPAKU]]

Predicting how a protein's [[wikipedia:amino acid|amino acid]] sequence folds into its three-dimensional native structure is a long-standing problem in structural biology, since a protein's shape largely determines its biological function. Because realistic simulations of protein folding require enormous amounts of computation, TANPAKU distributed this workload across volunteers' home computers using the BOINC platform, in the same manner as contemporaries such as [[Docking@Home]] and [[SIMAP]].

The project's stated goal was to use a computational technique called Brownian dynamics, developed specifically with distributed computing in mind, to simulate the folding pathways of small model peptides and proteins.<ref name="setigermany">{{Cite web |title=TANPAKU |url=https://www.seti-germany.de/wiki/TANPAKU |website=SETI.Germany Wiki |access-date=12 July 2026}}</ref>

== Scientific method ==
[[File:Brownian motion large.gif|thumb|An animated illustration of Brownian motion, the physical phenomenon underlying the Brownian dynamics simulation method used by TANPAKU]]

TANPAKU's simulations were built on the Brownian dynamics approach, an implicit-solvent simulation technique in which the explicit motion of solvent molecules is replaced by a combination of a systematic force, a frictional drag term, and a random ("Brownian") displacement representing collisions with solvent molecules. The general algorithm, first formulated for many-particle systems by Ermak and McCammon, updates each particle's position according to an equation of the form

<math>\mathbf{r}_i(t+\Delta t) = \mathbf{r}_i(t) + \frac{D_i}{k_B T}\mathbf{F}_i(t)\,\Delta t + \mathbf{R}_i(\Delta t)</math>

where <math>\mathbf{r}_i</math> is the position of particle <math>i</math>, <math>D_i</math> is its diffusion coefficient, <math>k_B</math> is the [[wikipedia:Boltzmann constant|Boltzmann constant]], <math>T</math> is temperature, <math>\mathbf{F}_i</math> is the systematic force acting on the particle, and <math>\mathbf{R}_i</math> is a random displacement with zero mean satisfying <math>\langle \mathbf{R}_i^2 \rangle = 6 D_i \Delta t</math>.<ref name="ermak">{{Cite journal |last1=Ermak |first1=Donald L. |last2=McCammon |first2=J. A. |title=Brownian dynamics with hydrodynamic interactions |journal=The Journal of Chemical Physics |volume=69 |issue=4 |pages=1352-1360 |year=1978 |doi=10.1063/1.436761}}</ref>

Working from this general framework, the TANPAKU team developed an atomistic Brownian dynamics implementation with a multiple time step integrator, allowing longer simulation timescales than a conventional [[wikipedia:molecular dynamics|molecular dynamics]] simulation with explicit water molecules would permit.<ref name="mts2003">{{Cite journal |last1=Ando |first1=Tadashi |last2=Meguro |first2=Toshiyuki |last3=Yamato |first3=Ichiro |title=Multiple Time Step Brownian Dynamics for Long Time Simulation of Biomolecules |journal=Molecular Simulation |volume=29 |issue=8 |pages=471-478 |year=2003 |doi=10.1080/0892702031000120528 |url=https://www.tandfonline.com/doi/abs/10.1080/0892702031000120528}}</ref> They subsequently applied the method to fold small model peptides, including a 13-residue [[wikipedia:alpha helix|α-helical]] peptide and a 12-residue β-hairpin peptide, from extended starting conformations to structures resembling their native folds.<ref name="freeenergy2005">{{Cite journal |last1=Ando |first1=Tadashi |last2=Yamato |first2=Ichiro |title=Free energy landscapes of two model peptides: alpha-helical and beta-hairpin peptides explored with Brownian dynamics simulation |journal=Molecular Simulation |volume=31 |issue=10 |pages=683-693 |year=2005 |doi=10.1080/08927020500183257 |url=http://www.tandfonline.com/doi/abs/10.1080/08927020500183257}}</ref>

[[File:AlphaHelixProtein.jpg|thumb|left|A ribbon depiction of an α-helical protein structure, one of the classes of model peptide folded in Ando and Yamato's Brownian dynamics studies]]

The volunteer-computing implementation of this method was described by Ando and Yamato in a 2007 conference paper, which framed Brownian dynamics as particularly well suited to distributed, volunteer-based computation because individual trajectories can be simulated largely independently of one another.<ref name="frontiers2007">{{Cite journal |last1=Ando |first1=Tadashi |last2=Yamato |first2=Ichiro |title=Brownian Dynamics Approach to Protein Folding |journal=Frontiers of Computational Science |year=2007 |doi=10.1007/978-3-540-46375-7_19 |url=http://link.springer.com/10.1007/978-3-540-46375-7_19}}</ref>

== Organization ==
TANPAKU was developed jointly by two laboratories at the Tokyo University of Science's Noda Campus: the Yamato Laboratory in the Department of Biological Science and Technology, led by Ichiro Yamato, and the Takeda Laboratory in the Department of Information Sciences.<ref name="deWiki" /><ref name="setigermany" /> Tadashi Ando, a researcher in the Yamato Laboratory, was the project's principal developer and main point of contact with the BOINC community.<ref name="thread3056">{{Cite web |title=Project TANPAKU |url=https://boinc.berkeley.edu/forum_thread.php?id=3056 |website=BOINC Message boards |access-date=12 July 2026}}</ref>

== History ==
=== Launch ===
TANPAKU opened for public participation on 7 July 2006.<ref name="boincnews" /> Prior to the BOINC-based project, Ando, Yamato, and collaborator Toshiyuki Meguro had spent several years developing and refining the underlying multiple time step Brownian dynamics method, publishing early results in ''Molecular Simulation'' in 2003 and 2005.<ref name="mts2003" /><ref name="freeenergy2005" />

=== Server failure and shutdown ===
On 18 August 2008, the TANPAKU server suffered an unexpected hardware failure and went offline.<ref name="thread3056" /> Project volunteers on the BOINC message boards reported the outage within days, and TANPAKU staff confirmed the failure and stated that repairs were underway, but further updates from the team were sparse over the following weeks.<ref name="thread3056" /> By late September 2008, volunteers with unsent work still queued on their computers began to suspect the project had been abandoned.<ref name="thread3056" /> In late September, Ando replied to a volunteer's inquiry to say he was out of the country and would follow up with collaborators in Japan, and in October a professor in the Department of Information Sciences confirmed that broken computers were being replaced and a new service was being prepared.<ref name="thread3056" />

No further public updates followed. By February 2009, a volunteer who examined the project's homepage found it had been reduced to a Japanese-language notice indicating that the project would not be reactivated, alongside a results page summarizing outcomes from the completed work.<ref name="thread3056" /> Community members reported shortly afterward that project staff had confirmed the project was over and that TANPAKU's researchers had moved on to other work.<ref name="thread3056" /> TANPAKU was never restarted, and by March 2009 it was regarded by the BOINC community as permanently discontinued.<ref name="thread3056" />

== Publications ==
The following publications, listed on the official [[wikipedia:BOINC|BOINC]] projects publication page, report scientific results arising from TANPAKU's Brownian dynamics computing.

=== Papers using TANPAKU-computed data ===
# {{Cite journal |last1=Ando |first1=Tadashi |last2=Yamato |first2=Ichiro |title=Free energy landscapes of two model peptides: alpha-helical and beta-hairpin peptides explored with Brownian dynamics simulation |journal=Molecular Simulation |volume=31 |issue=10 |pages=683-693 |year=2005 |doi=10.1080/08927020500183257 |url=http://www.tandfonline.com/doi/abs/10.1080/08927020500183257}}
# {{Cite journal |last1=Ando |first1=Tadashi |last2=Yamato |first2=Ichiro |title=Brownian Dynamics Approach to Protein Folding |journal=Frontiers of Computational Science |year=2007 |doi=10.1007/978-3-540-46375-7_19 |url=http://link.springer.com/10.1007/978-3-540-46375-7_19}}

=== Other project-related publications ===
The following earlier paper, by the same research group, describes the multiple time step Brownian dynamics method that TANPAKU's simulations were later built on, though it predates the BOINC-based project itself.
# {{Cite journal |last1=Ando |first1=Tadashi |last2=Meguro |first2=Toshiyuki |last3=Yamato |first3=Ichiro |title=Multiple Time Step Brownian Dynamics for Long Time Simulation of Biomolecules |journal=Molecular Simulation |volume=29 |issue=8 |pages=471-478 |year=2003 |doi=10.1080/0892702031000120528 |url=https://www.tandfonline.com/doi/abs/10.1080/0892702031000120528}}

== See also ==
* [[BOINC]]
* [[Docking@Home]]
* [[SIMAP]]
* [[wikipedia:Protein folding|Protein folding]]
* [[wikipedia:Brownian dynamics|Brownian dynamics]]
* [[wikipedia:Molecular dynamics|Molecular dynamics]]

== External links ==
* {{URL|http://issofty17.is.noda.tus.ac.jp/}} (former project homepage, largely offline)

== References ==
{{Reflist}}

[[Category:Completed BOINC projects]]
[[Category:Structural biology]]
[[Category:Volunteer computing projects based in Japan]]

TANPAKU - Revision history

Al Piskun: first light