Abstract
PeerMD, a P2P molecular dynamics simulation framework based on Web services is proposed. It utilizes rich free CPU time and network bandwidth of P2P networks to provide enough resources for dynamics simulation of bio-macromolecule, and has resolved the problem that it is difficult to interoperate between heterogeneous peers in P2P environment through Web services. Structure of PeerMD is given. Function, input and output of molecular dynamics simulation Web service are defined. Processes of publishing, discovering and invoking of molecular dynamics simulation Web service based on multi-level SuperPeer are given. A protocol system of PeerMD is implemented on a basic P2P platform JXTA, and experimental simulations of tumor necrosis fact alpha (TNF-α) and two mutations of it are executed on the protocol system. Simulation results show that PeerMD can speed up molecular dynamics simulation perfectly.
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References
Gasteiger J. Cheminformatics [M]. Verlag GmbH: Viley-VCH Press, 2004.
Brooks B R, Bruccoleri R E, Olafson B D, et al. CHARMM: A Program for Macromolecular Energy, Minimization and Dynamics Calculations [J]. Computational Chemistry, 1983, 4(2): 187–217.
Larson S M, Snow C D, Shirts M, et al. Folding@Home and Genome@Home: Using Distributed Computing to Tackle Previously Intractable Problems in Computational Biology [M]. Pittsburgh: Horizon Press, 2004.
Gower M, Cohen J, Phillips J, et al. Managing Bimolecular Simulations in a Grid Environment with NAMD-G [EB/OL]. [2008-03-21]. http://www.ks.uiuc.edu/Publications/Papers/PDF / GOWE2006/GOWE2006.pdf .
Wang Wenrui, Chen Guoliang, Xing Lirong, et al. Distributed Grid Computing Framework and Application in Molecular Dynamics Simulation[J]. Journal of Chinese Computer Systems, 27(7): 1326–1330(Ch).
Yue Kun, Wang Xiaoling, Zhou Aoying. Underlying Techniques for Web Services: A Surve[J]. Journal of Software, 2004, 14(3): 428–442 (Ch).
Li Ruixuan, Zhang Zhi, Wang Zhigang, et al. WebPeer: A P2P-based System for Publishing and Discovering Web Services [C]// International Conference on Services Computing. Orlando: IEEE Computer Society Press, 2005: 149–158.
Taima K, Electric S. Can We Ever Charge Napster Users[J]. IEEE Multi Media, 2002, 9(4): 76–81.
Ripeanu M. Peer-to-Peer Architecture Case Study: Gnutella Network[C]//First International Conference on Peer-to-Peer Computing. Linköpings: IEEE Computer Society Press, 2001: 99–100.
Yang B, Garcia M H. Designing a Super-Peer Network[C] // 19th International Conference on Data Engineering. Bangalore: IEEE Computer Society Press, 2003: 49–60.
Gong L. JXTA: A Network Programming Environment[J]. IEEE Internet Computing, 2001, 5(3): 88–95.
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Foundationitem: Supported by the National Natural Science Foundation of China(30670421, 60773191).
Biography: HUANG Baohua (1973–), male, Post Doctor, research direction: bioinformatics, Peer-to-Peer computing, information security, etc.
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Huang, B., He, L., Bao, Y. et al. PeerMD: A P2P molecular dynamics simulation framework based on Web services. Wuhan Univ. J. Nat. Sci. 13, 471–474 (2008). https://doi.org/10.1007/s11859-008-0418-4
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DOI: https://doi.org/10.1007/s11859-008-0418-4