TANPAKU

TANPAKU
Project
Status	Discontinued
Category	Structural biology
Compute	CPU
Development
Developer	Tadashi Ando, Ichiro Yamato (Yamato Laboratory); Takeda Laboratory
Author	Tadashi Ando
Sponsor	Tokyo University of Science
Initial release	August 2, 2005  (21 years ago)
Completed	No
Discontinued	August 18, 2008  (18 years ago)
Metadata
Website	http://issofty17.is.noda.tus.ac.jp/

TANPAKU was a Japanese BOINC volunteer computing project dedicated to protein folding and protein structure prediction research. The project was based at the 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. Its name comes from the Japanese word tanpaku-shitsu ( 蛋白質 ), meaning "protein".

TANPAKU's first server message was on August 2, 2005  (21 years ago) and opened for public participation on July 7, 2006  (20 years ago), when BOINC founder David P. Anderson announced that the project studied "protein structure and function using a novel method called Brownian Dynamics". 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

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 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.

Scientific method

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

${\mathbf{𝐫}}_i(t+\mathrm{\Delta }t)={\mathbf{𝐫}}_i(t)+\frac{D_i}{k_{B}T}{\mathbf{𝐅}}_i(t)\mathrm{\Delta }t+{\mathbf{𝐑}}_i(\mathrm{\Delta }t)$

where ${\mathbf{𝐫}}_i$ is the position of particle $i$, $D_i$ is its diffusion coefficient, $k_B$ is the Boltzmann constant, $T$ is temperature, ${\mathbf{𝐅}}_i$ is the systematic force acting on the particle, and ${\mathbf{𝐑}}_i$ is a random displacement with zero mean satisfying $⟨{\mathbf{𝐑}}_i^2⟩=6D_i\mathrm{\Delta }t$.

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 molecular dynamics simulation with explicit water molecules would permit. They subsequently applied the method to fold small model peptides, including a 13-residue α-helical peptide and a 12-residue β-hairpin peptide, from extended starting conformations to structures resembling their native folds.

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.

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. Tadashi Ando, a researcher in the Yamato Laboratory, was the project's principal developer and main point of contact with the BOINC community.

History

Launch

TANPAKU opened for public participation on 7 July 2006. 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.

Server failure and shutdown

On 18 August 2008, the TANPAKU server suffered an unexpected hardware failure and went offline. 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. By late September 2008, volunteers with unsent work still queued on their computers began to suspect the project had been abandoned. 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.

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. 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. TANPAKU was never restarted, and by March 2009 it was regarded by the BOINC community as permanently discontinued.

Publications

The following publications, listed on the official BOINC projects publication page, report scientific results arising from TANPAKU's Brownian dynamics computing.

Papers using TANPAKU-computed data

1. (2005).Free energy landscapes of two model peptides: alpha-helical and beta-hairpin peptides explored with Brownian dynamics simulation. Molecular Simulation. pp. 683-693. DOI: 10.1080/08927020500183257.
2. (2007).Brownian Dynamics Approach to Protein Folding. Frontiers of Computational Science. DOI: 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.

1. (2003).Multiple Time Step Brownian Dynamics for Long Time Simulation of Biomolecules. Molecular Simulation. pp. 471-478. DOI: 10.1080/0892702031000120528.

See also

• BOINC
• Docking@Home
• SIMAP
• Protein folding
• Brownian dynamics
• Molecular dynamics

External links

• http://issofty17.is.noda.tus.ac.jp/ (former project homepage, largely offline)