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Satoshi Matsuoka,
Hitoshi Sato,
Osamu Tatebe,
Michihiro Koibuchi,
Ikki Fujiwara,
Shuji Suzuki,
Masanori Kakuta,
Takashi Ishida,
Yutaka Akiyama,
Toyotaro Suzumura,
Koji Ueno,
Hiroki Kanezashi,
Takemasa Miyoshi
July 2014
Supercomputing Frontiers and Innovations: an International Journal: Volume 1 Issue 2, July 2014
Publisher: South Ural State University
Our claim is that so-called "Big Data" will evolve into a new era with proliferation of data from multiple sources such as massive numbers of sensors whose resolution is increasing expo- nentially, high-resolution simulations generating huge data results, as well as evolution of social infrastructures that allow for "opening up ...
Keywords:
Non-Volatile Memory, Extreme Computing and Big Data Convergence, Data Intensive Computing, Supercomputing, Big Data
2
September 2013
BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 1, Downloads (12 Months): 7, Downloads (Overall): 44
Full text available:
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Keywords:
protein-protein interaction, high-performance computing, protein docking
3
September 2013
BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Publisher: ACM
Bibliometrics:
Citation Count: 1
Downloads (6 Weeks): 7, Downloads (12 Months): 64, Downloads (Overall): 280
Full text available:
PDF
Protein-protein docking is a method for predicting the protein complex structure from monomeric protein structures. Because protein structural information has been increased and the application field has been expanded to more difficult ones such as interactome prediction, a faster protein-protein docking method has been eagerly demanded. MEGADOCK is fast protein-protein ...
Keywords:
GPGPU, fast Fourier transform, structural biology, protein-protein docking
4
September 2013
BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 1, Downloads (12 Months): 3, Downloads (Overall): 37
Full text available:
PDF
Keywords:
structural biology, template-based docking, protein-protein interaction, template-free docking
5
November 2012
SCC '12: Proceedings of the 2012 SC Companion: High Performance Computing, Networking Storage and Analysis
Publisher: IEEE Computer Society
Metagenome analysis is useful for not only understanding symbiotic systems but also watching environment pollutions. However, metagenome analysis requires sensitive sequence homology searches which require large computation time and it is thus a bottleneck in current metagenome analysis based on the data from the latest DNA sequencers generally called a ...
Keywords:
GPGPU, metagenomics
6
November 2012
PRIB'12: Proceedings of the 7th IAPR international conference on Pattern Recognition in Bioinformatics
Publisher: Springer-Verlag
We propose a new hydrophobic interaction model that applies atomic contact energy for our protein---protein docking software, MEGADOCK. Previously, this software used only two score terms, shape complementarity and electrostatic interaction. We develop a modified score function incorporating the hydrophobic interaction effect. Using the proposed score function, MEGADOCK can calculate ...
Keywords:
fast fourier transform, hydrophobic interaction, MEGADOCK, protein-protein docking, protein-protein interaction
7
August 2007
ISPA'07: Proceedings of the 5th international conference on Parallel and Distributed Processing and Applications
Publisher: Springer-Verlag
We have developed a high performance 3D convolution library for Protein Docking on IBM Blue Gene. The algorithm is designed to exploit slight locality of memory access in 3D-FFT by making full use of a cache memory structure. The 1D-FFT used in the 3D convolution is optimized for PowerPC 440 ...
8
February 2007
PDCN'07: Proceedings of the 25th conference on Proceedings of the 25th IASTED International Multi-Conference: parallel and distributed computing and networks
Publisher: ACTA Press
We introduce a parallelized molecular dynamics (MD) simulation adapted for the IBM Blue Gene/L supercomputer. We begin by describing the Parallel MD code. Next we discuss how Parallel MD was tuned for Blue Gene/L. We then show the results for some test targets, related to disease associated proteins, that we ...
Keywords:
molecular dynamics (MD) simulation, code optimization, high performance computing, scientific computing
9
April 2004
Bioinformatics: Volume 20 Issue 6, April 2004
Publisher: Oxford University Press
Motivation: Homology search is one of the most fundamental tools in Bioinformatics. Typical alignment algorithms use substitution matrices and gap costs. Thus, the improvement of substitution matrices increases accuracy of homology searches. Generally, substitution matrices are derived from aligned sequences whose relationships are known, and gap costs are determined by ...
10
March 2004
Bioinformatics: Volume 20 Issue 4, March 2004
Publisher: Oxford University Press
Summary: We present FORTE, a profile--profile comparison tool for protein fold recognition. Users can submit a protein sequence to explore the possibilities of structural similarity existing in known structures. Results are reported via email in the form of pairwise alignments. Availability: The server is available at http://www.cbrc.jp/forte/
11
May 2002
IEEE Intelligent Systems: Volume 17 Issue 3, May 2002
Publisher: IEEE Educational Activities Department
The authors propose a method for multidimensional distribution analysis using a data compression technique. The method avoids the explosion in number of parameters (or coefficients) representing a multidimensional distribution even when the distribution has many dimensions (up to six dimensions or more). In the method, a multidimensional distribution is linearly ...
Keywords:
linear compression, mean-force potentials, multidimensional distribution, spherical Bessel, spherical harmonics
12
May 2000
HPC '00: Proceedings of the The Fourth International Conference on High-Performance Computing in the Asia-Pacific Region-Volume 2 - Volume 2
Publisher: IEEE Computer Society
In this paper, we report on the design and the implementation of ESCAPE 2.0, the parallel exhaustive conformational search system of peptides. We employed an exhaustive search method for conformational searches, so that ESCAPE 2.0 does not overlook any important conformations that may be overlooked by other systems. Although the ...
13
May 2000
HPC '00: Proceedings of the The Fourth International Conference on High-Performance Computing in the Asia-Pacific Region-Volume 2 - Volume 2
Publisher: IEEE Computer Society
In this paper, we describe the design and the MPI-implementation of two parallel tree code molecular dynamics programs called the MolTreC and the Treecode AMBER, respectively. Both programs were developed using the parallel Barnes-Hut tree code for calculating Coulomb inter-actions, which have been developed in earlier work. The parallel programs ...
14
May 1999
ISHPC '99: Proceedings of the Second International Symposium on High Performance Computing
Publisher: Springer-Verlag
15
November 1997
ISHPC '97: Proceedings of the International Symposium on High Performance Computing
Publisher: Springer-Verlag
16
November 1997
ISHPC '97: Proceedings of the International Symposium on High Performance Computing
Publisher: Springer-Verlag
17
June 1997
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology
Publisher: AAAI Press
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