ポスターセッション
討論時間 奇数番号：9/18 17:00-18:00 偶数番号：9/18 18:00-19:00

1. 分子計算
101

Computational Chemistry Investigation of Water Interface in Colloidal
Systems
Ugur Mart1, Ryuji Miura1, Chang-ho Jung1, Takahiro Oyama1, Akira Endou 1, Momoji Kubo 1,
Akira Miyamoto 1,2(Dept. of Appl. Chem., Tohoku Univ. 1, NICHe, Tohoku Univ. 2)

102

Effect of organic moieties on the acidic properties of zeolite with an organic
lattice as a new candidate for drug synthesis
Mohamed Elanany1, Akira Endou1, Momoji Kubo1 and Akira Miyamoto1,2(1Department of Applied Chemistry, Graduate School of Engineering, Tohoku University,
2
New Industry Creation Hatchery Center, Tohoku University)

103

Theoretical Investigation of Excited State and Excitation Processes for
Several Compounds
Xiaojing Wang1, Lv Chen1, Akira Endou1, Momoji Kubo1, Akira Miyamoto1,2(Dept. Appl. Chem. Tohoku Univ. 1, NICHE Tohoku Univ. 2)

104

Computational Study on the Conformation of the Complex of Lipase
Enzyme with Foreign Organic Substrate
Yoshinobu Naoshima1, Yoshihiro Mori2, Takatomo Kimura3, Makoto Kamezawa3, Hojun
Tachibana3, and Takehiko Ohtani3(Okayama University of Science1, Graduate School of Okayama University2, and Konan
Chemical Industry Co., Ltd.3)

105

Protein-ligand flexible docking method for in silico screening
Yoshifumi Fukunishi1 , Haruki Nakamura1,2(Japan Biological Information Research Center (JBIRC), National Institute of Advanced
Industrial Science and Technology (AIST) 1, Institute for protein Research, Osaka University 2)

106

Molecular dynamics simulation of reaction mechanism of thehyperthermophilic aspartate racemase
Tomohiro Seko1, Lijun Liu2, Takumitsu Yoshida3, Kunio Miki2, Masafumi Yohda3(Fuji Xerox Co., Ltd.1, Graduate School of Science, Kyoto University2, Faculty of Engineering,Tokyo University of Agriculture and Technology 3)

107

Harmonic Force Field Parameterization based on Hessian matrix
Hirotaka Ohde1, Daisuke Katagiri1, Hidenori Ishikawa1, Saburou Neya1, Masayuki Hata1, Tyuji
Hoshino1(Graduate School of Pharmaceutical Sciences, Chiba University1)

108

Development of a molecular dynamics simulation system : prestoX

Yoshiaki Mikami1,2, Yoshifumi Fukunishi1, Ikuo Fukuda1,2, Jae Gil Kim1,2, Rie Tatsumi1,2,
Haruki Nakamura1,3(Biological Information Research Center (BIRC), National Institute of Advanced Industrial
Science and Technology (AIST) 1, Japan Biological Information Research Center (JBIRC),
Japan Biological Informatics Consortium (JBIC) 2, Institute for Protein Research, Osaka
University 3)

109

Parallelization of Biomolecular Simulations through Replica Exchange
Molecular Dynamics
Masakatsu Ito1,2, Umpei Nagashima1,2(1Research and Development for Applying Advanced Computational Science and Technologyof Japan Science and Technology Corporation, 2Grid Technology Research Center, National
Institute of Advanced Industrial Science and Technology (AIST))

110Interaction analysis for SARS virus proteinase and its ligands with abinitio FMO method
Shinji Amari1, Mayuko Takeda-Shitaka2, Mitsuo Iwadate2, Norio Yamamoto3, Nobutaka Fujii4,
Naoki Yamamoto3, Hideaki Umeyama2, Tatsuya Nakano5(University of Tokyo1, Kitasato University2, Tokyo Medical and Dental University3, Kyoto
University4, National Institute of Health Sciences5)111

BioStation Dock: Application of protein-ligand docking to screen
compounds
Toshiyuki Sato1,2, Ikuo Okouchi1,2, Kaori Fukuzawa1,2, Kozo Aoki3, Kazuo Koyano1, Shinji
Amari3, Katsuki Amemiya1, and Tatsuya Nakano4(AdvanceSoft Corporation 1, Fuji Research Institute Corporation2, University of Tokyo3, andNational Institute of Health Sciences 4)112

Periodical Boundary Computational Chemistry Studies on Tribology
Chemistry Reaction
Hui. Zhou1, Akira Endou1, Momoji Kubo1, Akira Imamura2, Akira Miyamoto1,3(Graduate School of Engineering, Tohoku Univ. 1, Faculty of engineering, Hiroshima Kokusai
Gukuin Univ.2, New Industry Creation Hatchery Center, Tohoku Univ. 3)

113

Study on Photocatalytic Processes by Accelerated Quantum Chemical
Molecular Dynamics Method
Chen Lv1, Xiaojing Wang1, Tomonori Kusagaya1, Akira Endou 1, Momoji Kubo1, Akira
Imamura2, and Akira Miyamoto1,3(Department of Applied Chemistry, Tohoku University1, Faculty of Engineering, Hiroshima
Kokusai Gakuin University2, NICHe, Tohoku University3)

114

Accelerated quantum chemical molecular dynamics simulation and DFT
studies on the catalytic reaction of lanthanocene
Yi Luo1, Yuki Ito1, Hitoshi Kurokawa1, Akira Endou1, Momoji Kubo1, Akira Imamura2, andAkira Miyamoto1,3(Department of Applied Chemistry, Tohoku University1, Faculty of Engineering, Hiroshima
Kokusai Gakuin University2, NICHe, Tohoku University3)115

Dynamic Observation of Nucleic Acid Structure by Molecular Dynamics
Satoshi Fujii, Takahiko Nojima and Shigeori Takenaka(Department of Applied Chemistry, Faculty of Engineering, Kyushu University)

116

Accelerated Quantum Chemical Molecular Dynamics Study on theUnsaturated Hydrocarbon Polymerization
Huifeng Zhong1, Masaki Fushimi2, Akira Endou1, Momoji Kubo1, Akira Imamura3, and Akira
Miyamoto1,4(Dept. Appl. Chem., Tohoku Univ 1. Oita Research Center, R&D Department, SunAllomer Ltd2.
Fac. Eng., Hiroshima Kokusai Gakuin Univ 3. NICHe, Tohoku Univ 4.)

117

MD simulation of asymmetric phospholipid bilayers (POPC/POPE-POPS)
with the physiological concentration of ions and cholesterols
Kenichi Mori, Masayuki Hata, Saburo Neya, Tyuji Hoshino(Graduate School of Pharmaceutical Sciences, Chiba University)

118

Biosystem Modeling from Micro-Scale to Macro-Scale
Momoji Kubo 1, Kotaro Ohkushi 1, Yasuyuki Suzuki 1, Akira Endou 1, Kazumi Nishijima 2,3,
Eiichiro Ichiishi 3, Masahiro Kohno 3, and Akira Miyamoto 1,3(Department of Applied Chemistry, Tohoku University 1, Pharmaceutical Consortium forProtein Structure Analysis 2, NICHe, Tohoku University 3)

119

Development of accelerated quantum molecular dynamics program“Colors” into lanthanide compounds
Yuki Ito1, Chang-ho Jung1, Yi Luo1, Akira Endou1, Momoji Kubo1, Akira Imamura2, Akira
Miyamoto3(Dept. Appl. Chem., Tohoku University1, Hiroshima Kokusai Gakuin University2, NICHe,
Tohoku University3)

120

Development of Kinetic Monte Carlo Simulator and Its Application to
Analysis of Mass Transfer and Diffusion Phenomenon
Akira Endou1, Hitoshi Kurokawa1, Ryuji Miura1, Momoji Kubo1, and Akira Miyamoto1, 2(Grad. School of Eng., Tohoku Univ. 1, NICHe, Tohoku Univ. 2)

121

Prediction of the Lubricous Characteristic by Computational Chemistry
Yohei Toyoda1, Daisuke Kamei1, Akira Endou1, Momoji Kubo1, Akira Miyamoto1,2(Dept. Appl. Chem., Tohoku Univ. 1, NICHe, Tohoku Univ. 2)

122Development of Quantum Chemical Simulation System for Proteins,
ProteinDF

Fumitoshi Sato1, Naoki Ihara1, Tetsuya Ueno1, Hiroyuki Otsuki1, Tomoyuki Kinjo1, Saisei
Tahara1, Naoki Tsunekawa1, Yasuyuki Nishimura1, Hajime Muta1, Tamotsu Yoshihiro1, Chong
Hwang Lean1, Yoshitaka Nishikawa3, Sinya Muramatsu3, Kazutoshi Okada3, Toru Inaba2, So
Koike2, Yasuo Nagamine2, Hideaki Koike2, Hiroshi Kashiwagi1,2(Institute of Industrial Science, University of Tokyo1, AdvanceSoft Corporation2, Fuji ResearchInstitute Corporation3)

123

Theoretical Studies of Binding of Mannose-binding Protein to
Monosaccharides
Sachiko Aida-Hyugaji1,2, Keiko Takano2, Toshikazu Takada3, Haruo Hosoya2, Naoya Kojima1,
Tsuguo Mizuochi1, and Yasushi Inoue1(Tokai University1, Ochanomizu University2, NEC3)

124

The Simulation of Helix-Coil Transition by MD Caluculations
Yoshiro Nakata, Masami Uno(Department of Biophysics, Faculty of Engineering, Gunma University)

125

Development of a Geometry Optimization Program for Proteins Based on
ProteinDF System
Tomoyuki Kinjo1, Naoki Ihara1, Naoki Tsunekawa1, Kazutoshi Okada2,
Nobutaka Nishikawa2, Tetsuya Ueno1, Fumitoshi Sato1, Hiroshi Kashiwagi1,3(Institute of Industrial Science, University of Tokyo1, Fuji Research Institute Corporation2,
Advance Soft3)

126

Temperature dependent kinetics and mechanism of the protein folding in acoarse-grained model using the native structure information
Hironori K. Nakamura1,2, Mitsunori Takano1(Dept. of Life Sci., Grad. Sch. of Arts & Sci., Univ. of Tokyo 1, ACT-JST, JST2)

127

Fragment molecular orbital study for the interaction between cAMP
receptor protein and DNA
Kaori Fukuzawa1, Yuto Komeiji2, Yasuo Sengoku3, Katsumi Omagari4, Mitsuo Takano4, Akira
Suyama4, Shigenori Tanaka5, and Tatsuya Nakano6(Fuji Research Institute Corporation1, National Institute of Advanced Industrial Science andTechnology2, Toyohashi University of Technology3, The University of Tokyo4, Toshiba
Corporation5, National Institute of Health Sciences6)

128

A Theoretical Study on Proton Transport
Kazunori Bada1, Yusuke Makino1, Hitoshi Kurokawa1, Akira Endou1, Momoji Kubo1, andAkira Miyamoto1,2(Department of Applied Chemistry, Graduate School of Engineering, Tohoku University 1, New
Industry Creation Hatchery Center, Tohoku University2)

129

Molecular dynamics of C30 region in α-Lactalbumin
Yuji Kitai1, Masashi Sonoyama2, Yoichi Hagiwara1, Matsuaki Terada1, Kenta Nakai3, Shigeki
Mitaku2(Tokyo University of Agriculture and Techcology 1, Nagoya University2, The Institute ofMedical Science, The University of Tokyo3)

130

Application of Fragment Molecular Orbital Method to Calculations on
Proteins with Zinc AtomTakanori Harada1, Tatsuya Nakano2, Hiroaki Tokiwa1(Rikkyo University1, National Institute of Health Sciences2)

131

Development of New Kinetic Monte Carlo Simulator for Ion Transport
Hitoshi Kurokawa1, Kazunori Bada1, Yusuke Makino1, Akira Endou1, Momoji Kubo1, andAkira Miyamoto1, 2(Department of Applied Chemistry, Graduate School of Engineering, Tohoku University 1, New
Industry Creation Hatchery Center, Tohoku University2)132

Computational Chemistry Study of Metal Complexes: Structures andReaction Dynamics
Rado RAHARINTSALAMA1, Hiroaki MUNAKATA2, Akira ENDOU2, Momoji KUBO2
Akira MIYAMOTO1,2(Dept. of Appl. Chem., Tohoku Univ. 1, NICHe, Tohoku Univ. 2)

133

Accelerated quantum chemical molecular dynamics study on electronic
properties of platinum cluster in water environment
Changho Jung1, Akira Endou1, Momoji Kubo1, Akira Imamura2 and Akira Miyamoto1,3(Department of Applied Chemistry, Tohoku University1, Hiroshima Kokusai Gakuin
University2, New Industry Creation Hatchery Center (NICHe)3)

134

On the collective motion of macromolecules
Takashi Nakamura(College of Industrial Technology, Nihon University)

135

Atomic Structures and Electronic States of Water Clusters: A
Computational Chemistry Study
Yoko Watanabe1, Daisuke Kamei1, Takahiro Oyama1, Ryuji Miura1, Akira Endou1, Momoji
Kubo1, Tomohiro Ogawa2, Akira Miyamoto1, 3(Dept. Appl. Chem., Tohoku Univ. 1, Tokyo Electric Power Company2, NICHe, Tohoku Univ. 3)

136

Large Scale Quantum Chemical Molecular Dynamics of Surface Reaction
with Ion Implantation
Katsumi Sasata1, Akira Endou1, Momoji Kubo1, Akira Imamura2, Akira Miyamoto1,3(Tohoku Univ.1, Hiroshima Kokusai Gakuin Univ.2, NICHe, Tohoku Univ. 3)

137

Application of Accelerated Quantum Molecular Dynamics Method to theInvestigation on the Electrode / Organic Molecules Interface

Yuhsuke Makino1, Ken Suzuki1, Akira Endou1, Momoji Kubo1, Akira Imamura2, and Akira
Miyamoto1, 3(Grad. School of Eng., Tohoku Univ. 1, Dept. Eng., Hiroshima Kokusai Gakuin Univ. 2, NICHe,
Tohoku Univ.3)

138

Conformational Change of Calmodulin by Ca2+ and Peptide Removal
Li Hongzhen1, Kiyonobu Yokota2, Kenji Satou1,2(Institute for Bioinformatics Research and Development (BIRD), Japan Science andTechnology Corporation (JST)1, School of Knowledge Science, Japan Advanced Institute of
Science and Technology2)

139

Computational Chemistry Study for Nanoscale Tribology
Takahiro Oyama 1, Akira Endou1, Momoji Kubo1, Akira Miyamoto1,2(Dept. of Appl. Chem., Tohoku Univ. 1, NICHe, Tohoku Univ. 2)

2. 創薬テクノロジー
201

SOLUTION STRUCTURE OF CHITINASE-ARGIFIN COMPLEXSTUDIED BY MOLECULAR DYNAMICS
Hiroaki Gouda 1, Shuichi Hirono 1(School of Pharmaceutical Sciences, Kitasato University1)

202

Development of conformational search algorithm for proteins
Toshiyuki Kamakura, Hitoshi Gotoh(Toyohashi University of Technology)

203

Conformational Analyses of a β-Turn Peptide by Brownian Dynamics
Simulation
Noriyuki Yamaotsu, Shuichi Hirono(School of Pharmaceutical Sciences, Kitasato University)

204

Generation of a novel equation for logP estimation using a neural network
Sumie Tajima1, Kenji Yamagishi2, Makoto Haraguchi1, Umpei Nagashima3(Bestsystems Inc.1, Rikkyo University2, Grid Technology Research Center3)

205

Integrated In Silico Screening (III) : Human P450 Prediction Model
Construction and Investigation
Masato Kitajima1 Jose Martin Ciloy1 Kohtaro Yuta2(Fujitsu kyushu system engineering limited 1 Fujitsu limited2 )206

Prediction of Protein-Ligand Interactions from molecular, sequence andstructure descriptors
Shandar Ahmad and Akinori Sarai(Kyushu Institute of Technology)

207

Development of a Protein-Ligand Interaction Database, ProLINT, and Its
Application to QSAR Analysis
Kouji Kitajima1 , Shandar Ahmad1, Hideo Kubodera2, Shinji Sunada3, Akinori Sarai1(Kyushu Institute of Technology1, ZeoGene2, Mitsubishi Pharma3)

208

The structure –activity relationship of P-glycoprotein using Chemical
Fragment codes
Hiroyuki Hirano1, Yuko Onishi1,2, Toshihisa Ishikawa2(GS platZ Co., Ltd. 1, Tokyo Institute of Technology2)

209

A Functional Study on Genetic Polymorphisms of P-Glycoprotein(ABCB1)
Toshihisa Ishikawa, Aki Sakurai, and Yuko Onishi(Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology)

210

A Functional Study on Genetic Polymorphisms of ABCG2
Toshihisa Ishikawa1, Hideyuki Mitomo1, Yuko Hagiwara1, Shiho Kasamatsu1, Yuko Onishi1,
Akiko Ito2, Megumi Yoshikawa2, and Yoji Ikegami2(1Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology,2
Department of Drug Metabolism and Disposition, Meiji Pharmaceutical University)

211

Development of a high-throughput screening system for the substratespecificity of human P-glycoprotein (ABCB1)
Yuko Onishi1,3, Keisuke Oosumi2, Hiroyuki Hirano3, Makoto Nagakura2, Shigeki Tarui3,
Toshihisa Ishikawa１(Tokyo Institute of Technology1,Biotec Co.,Ltd.2,GS PlatZ Co.,Ltd.3)

212

Homology modeling of human acetylcholine receptor using FAMS
Ligand&Complex
Mayuko Takeda-Shitaka, Daisuke Takaya, Hirokazu Tanaka, Mitsuo Iwadate and Hideaki
Umeyama(School of Pharmaceutical Sciences, Kitasato University)

213

Prediction of Inhibition Mechanism of Thymidine Phosphorylase with
Water Molecules in Active Site
Yukio Tada 1, Shingo Yano 1, Hideki Kazuno1, Tsutomu Sato 1, Masakazu Fukushima 1, Tetsuji
Asao 1(Hanno Research Center, Taiho Pharmaceutical Co., Ltd.1)

3. 分子生物学における情報計算技法
301

Analysis of Cation-π Interactions in Membrane Protein Structures
M. Michael Gromiha and Makiko Suwa
(Computational Biology Research Center (CBRC),National Institute of Advanced Industrial
Science and Technology (AIST))302

Development of HocDB (Homology-based clustering DataBase), a sequenceclassification system for database searching
Motokazu Ishikawa1, Yoshinori Sato1, Hiroyuki Toh2
(Mitsubishi Space Software Co. Ltd1, Bioinformatics Center, Institute for Chemical Research,
Kyoto University2)

303

Development of Lossless Compression Techniques for Biology Informationand its Application for Bioinformatics Database Retrieval
Toshio Modegi(Research & Development Center, Dai Nippon Printing Co., Ltd.)

304

Bioinformatic Analyses of Transcription Factors
Akinori Sarai1, Samuel Selvaraj2, Michael M. Gromiha3 and Hidetoshi Kono4(1Kyushu Institute of Technology, 2Bharathidasan University, India, 3Computational Biology
Research Center, 4Japan Atomic Energy Research Institute.)

305

Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNIT):
Developments in 2003.
M. D. Shaji Kumar1, Ponraj Prabakaran2, Hatsuho Uedaira1, M. Michael Gromiha3, Kouji
Kitajima1 and Akinori Sarai1(Kyushu Institute of Technology 1, NIH, USA2, CBRC, AIST3)

306

Protherm: Thermodynamic Database for Proteins and Mutants
K. Abdulla Bava1, M. Michael Gromiha2, Hatsuho Uedaira1, Koji Kitajima1,and Akinori Sarai1(1Kyushu Institute of Technology, 2Computational Biology Research Center)

308

Identification of Target Genes of the Orphan Nuclear Receptor PPAR
Hiroki Momose 1, Tuguchika Kaminuma2, Yoshitomo Tanaka1, Kotoko Nakata3, Hiroshi
Tanaka4(Graduate School of Tokyo Medical and Dental University 1, Biodynamics Inc.2, National
Institute of Health Sciences3, Medical Research Institute, Tokyo Medical and Dental
University4)309

Monte Carlo simulation studies on biochemical systems
Ryuzo Azuma1, Tomoyuki Yamamoto2, Yoshiki Yamaguchi1, Akihiko Konagaya1(Genomic Sciences Center, RIKEN1, School of Knowledge Sci. JAIST 2)

310

A high-speed search method for distributed and federated XML databases
Shin'ichi Tsuji 1,2, Yasuhiko Nakashima1,2, Kenji Satou1, Fumikazu Konishi3, Akihiko
Konagaya3(JAIST School of Knowledge Science 1, NEC Software Hokuriku, Ltd. 2, RIKEN Genomic
Sciences Center3)

311

Analysis of Similar Structural Protein with Low Sequence Identity by
Coarse-Grained Charge Distribution in Sequence
Kenichiro Imai, Shigeki Mitaku(Division of Applied Physics Graduate School of Engineering Nagoya University)

312

Development of a structure based protein function prediction
Takeo Asaoka1, Tadashi Ando2, Toshiyuki Meguro3, Ichiro Yamato4(Department of Biological Science and Technology, Tokyo University of Science)

313

A distributed and autonomous job dispatcher for OBIEnv
Yasuhiko Nakashima 1,2, Kenji Satou 1, Shin'ichi Tsuji 1,2, Xavier Defago 3, Akihiko Konagaya 4(JAIST School of Knowledge Science 1, NEC Software Hokuriku, Ltd 2,JAIST School ofInformation Science 3,RIKEN Genomic Sciences Center 4)314

Identification of Nuclear Receptor Target Genes Related to Drug-Drug
Interaction
Yoshitomo Tanaka1, Tuguchika Kaminuma2, Hiroki Momose1, Kotoko Nakata3, Hiroshi
Tanaka4(Graduate School of Tokyo Medical and Dental University 1, Biodynamics Inc.2, National
Institute of Health Sciences3, Medical Research Institute, Tokyo Medical and Dental
University4)

315

PROMISS: Protein identification support tool for MS analysis data
Aki Hasegawa, Kazumi K. Matsumura, Akihiko Konagaya(Bioinformatics Group, GSC, RIKEN)

316

Structural Analysis of Metabolic Networks: Format Describing
Intermetabolite Atom-Level Connectivity
Jun Ohta(Okayama University Graduate School of Medicine and Dentistry)

318

Classification of Protein Structures Using PDB-REPRDB system
Noguchi Tamotsu(Computational Biology Research Center (CBRC), AIST)

320

Feature Representation and Kernel Selection in Prediction of ProteinProtein Interaction Sites Using Support Vector Machine
Gaku Keyakidani1, Kiyonobu Yokota1, Yuichiro Nishida1, Kenji Satou1,2(Japan Advanced Institute of Science and Technology 1,Institute for Bioinformatics Researchand Development (BIRD), JST2)

322

Methods of kinetic parameter estimation from time-courses in E-Cellparameter estimation tools
Shinichi Kikuchi1, Masahiro Sugimoto1, 2, Yoshiya Matsubara1, Mariko Ando1, and Masaru
Tomita1(Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University 1,
MITSUBISHI SPACE SOFTWARE CO., LTD. 2)

323

Prediction of Biochemical Reactions using Genetic Programming
Masahiro Sugimoto12, Kikuchi Shinichi1, Masaru Tomita1(Institute for Advanced Biosciences of Keio University 1,MITSUBISHI SPACE SOFTWARE
CO., LTD.2)

324

Analysis of transmembrane segment for membrane protein discrimination
Toshiyuki Tsuji 1, Shigeki Mitaku1(Division of Applied Physics Graduate School of Engineering Nagoya University 1)

4. ゲノムワイドな解析
401

Development of Method to Predict Protein Function of Escherichia coli
Using Protein Complex Data
Seira Nakamura 1,6, Rintaro Saito 1, Takeshi Ara 1,2, Aya Itoh 1,2, Md. Arifuzzaman 3,4, Maki
Maeda 2, Taku Oshima 2,4, Chieko Wada 2,5, Hirotada Mori 1,2,4, Masaru Tomita 1,7(Institute for Advanced Biosciences, Keio University 1, CREST JST 2, NEDO 3,Research and
Education Center for Genetic Information, Nara Institute of Science and Technology 4, Institutefor Virus Research, Kyoto University 5, Bioinformatics Program, Graduate School of Mediaand Governance, Keio University 6, Faculty of Environmental Information, Keio University 7)

402

Gene expression analysis using Akaike’s Information Criterion
Koji Kadota and Katsutoshi Takahashi(Computational Biology Research Center (CBRC), AIST)

403

KAREIDMAP: Gene Regulatory Network Analysis Support System
Hironori Mizuguchi1, Dai Kusui1, Taku Oshima2, Shigehiko Kanaya3 and Hirotada Mori2,4(Internet Systems Research Laboratories, NEC Corporation1,Research and Education Center for
Genetic Information, Nara Institute of Science and Technology2,Graduate School ofInformation Science, Nara Institute of Science and Technology3,Institute for Advanced
Biosciences, Keio University4)

404

Prediction of Motif-Motif Interaction and Protein-Protein Interaction in
Escherichia coli
Hikaru Kimura1,3, Seira Nakamura1,2, Rintato Saito1, Takeshi Ara1,4, Aya Itoh1,4, Md
Arifuzzaman5,6, Maki Maeda4, Taku Oshima4,6, Chieko Wada4,7, Hirotada Mori1,4,6,
Masaru Tomita1,3(Institute for Advanced Biosciences, Keio University1, Bioinformatics Program, Graduate
School of Media and Governance, Keio University 2, Faculty of Environmental Information,
Keio University3, CREST, JST4, NEDO5, Research and Education Center for Genetic
Information, Nara Institute of Science and Technology6, Institute for Virus Research, Kyoto
University7)

405

Fundamental examination of data evaluation for Yeast cDNA microarray
Satomi MIZUKAMI1, Yoshiteru SUZUKI2, Hitoshi IWAHASHI3(Advanced Industrial Science and Technology (NEDO) 1,Advanced Industrial Science andTechnology2,Human Stress Signal Research Center3)

406

Transcriptome profiling and cluster analysis of Saccharomyces cerevisiae
under environmental stress conditions.
Yoshiteru Suzuki , Kim Hyun-Ju , Yuko Momose , Emiko Kitagawa , Takayuki Honma ,Sophon Shirisatta , Sakiko Kurita , Megumi Kojima , Parveen Meher , Shinzou Kimura , Junko
Takahasi , Hitoshi Iwahashi(National Institute of Advanced Industrial Science and Technology (AIST))407

The acquisition of freezing/thawing tolerance was caused by respiration
activity in mitochondria
Yoshinori Murata, Hitoshi Iwahashi, and Syuu-ichi Oka(International Patent Organism Depositary AIST)

408

Constructing Reliable Protein Complex Data of Saccharomyces cerevisiae
Rintaro Saito, Masaru Tomita(Institute for Advanced Biosciences, Keio University)

409

Assistance tool for MS/MS shotgun analysis
Chihiro Higuchi , Toshiyuki Mikami , Kazunori Yanagi , Jun Sakai , Shinichi Kojima ,Masaharu Kanaoka(Genomic Science Laboratories, Sumitomo Phamaceuticals Co., Ltd.)

410

cDNA microarray for human skeletal muscles to understand the molecularmechanism of myogenesis and myostatin effectSatoru Noguchi1, 2, Rumi Kurokawa1, 2, Masako Fujita1, 2, Toshifumi Tsukahara2, 3, Atsumi
Tsujimoto2, 4, Ichizo Nishino1, 2(National Institute of Neuroscience, National Center of Neurology and Psychiatry 1, CREST
JST2, Japan Advanced Institute of Science and Technology 3, DNA Chip Research Inc4.)

411

Profiling of genome-wide expression of protein translocation defect ofEscherichia coli
Hisayo Shimizu1, Hajime Tokuda2, Hitoshi Iwahashi1, Syuichi Oka1
(AIST International Patent Organism Depositary 1, Institute of Molecular and Cellular
Biosciences 2)412

Development of expression profile analysis tool SOSUIarray which is
focused on transmembrane proteins
Naoyuki Asakawa1, Shigeki Mitaku2(Tokyo University of Agriculture and Technology 1, Nagoya University2)

413

Ranking of Biological Pathway Using GSCope and Microarray Data
Yoshikazu Hasegawa1, Katsura Hirosawa1, Naoki Okamoto2,Tetsuro Toyoda1 and Akihiko
Konagaya1(Bioinformatics Group, GSC, RIKEN1, NEC Infomatec Systems Ltd2)414

Classification of stress-induced genomic expression profiles
Yuko Momose1, Hitoshi Iwahashi1, Shu-ichi Oka1
(The National Institute of Advanced Industrial Science and Technology (AIST) 1)

416

How to choose best probe set for oligo DNA microarrays?
Mikihiko Nimura 1, Masato Inoue1, Yasuyuki Hayashi1, Todd Richmond2, Michael Hogan2,
Steve Smith2, Roland Green2(GeneFrontier Corporation 1, NimbleGen Systems, Inc.2)

417

Development of Magtration® System 8Lx
Tomoyuki Hatano, Yuriko Tojo, Hironobu Satoh, Yoshinao Hirahara, Masaaki Takahashi,
Kimimichi Obata, Hideji Tajima(Precision System Science Co., Ltd., Matsudo, Japan)

418

Method for identification of transcription regulatory regions bycomparative genomics
Jiro Araki, Takeaki Taniguchi, Takehiko Ito(Mitsubishi Research Institute Inc.)

419

Automatic generation of cell-wide pathway model from complete genome
Kazuharu Arakawa1,2, Yohei Yamada1,3, Hiromi Komai1,3, Kosaku Shinoda1,4, Yoichi
Nakayama1,3, Masaru Tomita1,3(Institute for Advanced Biosciences, Keio University 1, Bioinformatics Program, Graduate
School of Media and Governance 2, Department of Environmental Information3, Department of
Policy Management4)

420

G-language Genome Analysis Environment Version 2
Kazuharu Arakawa1,2, Ryo Hattori1,3, Yohei Yamada1,3, Yusuke Kobayashi1,3, Hayataro
Kouchi1,3, Atsuko Kishi1,3, Masaru Tomita1,3,(Institute for Advanced Biosciences, Keio University1, Bioinformatics Program, Graduate
School of Media and Governance 2, Department of Environmental Information3 )421

Homology search of proteins using non-additive entropy
Takahashi Koichi, Nakamura Naoki(Kinki University )422

More Conserved Upstream Sequences for Transcription Factor Genes andits Evolutionary Implication
Hisakazu Iwama1,2 and Takashi Gojobori1,2(1National Institute of Genetics, 2National Institute of Advanced Industrial Science andTechnology)

5. 医薬品開発と有害事象研究基盤
501

Ki Bank: A Database for Molecular Interaction Analysis between Proteins
and Chemicals
Junwei Zhang1, Masahiro Aizawa1, Kenji Onodera1, Shinji Amari1, Yoshio Iwasawa2 andKotoko Nakata3(1Collaborative Research Center of Frontier Simulation Software for Industrial Science,
Institute of Industrial Science, University of Tokyo; 2AdvanceSoft Corporation; 3Division of
Safety Information on Drug, Food and Chemicals, National Institute of Health Sciences)

502

Analysis and Prediction of Drug Excretion into Human Breast Milk (2nd)- Additional Analysis Including Hydrophilic Compounds Takashi Fujiwara, Yuki Hibino, Masaru Kihara, Aiko Yamauchi, Hiroshi Chuman(Graduate School of Pharmaceutical Sciences, The University of Tokushima)503

In situ Measurement for Apoptotic Carcinoma Cells Using by a Photon
Correlation Spectroscopy
Mayu Nakamura, Takahito Kawamura, Shintaro Obara, Hiroshi Takano and Masayuki Itoh
(Department of Chemical Engineering and Materials Science, Doshisha University)

504

Kinetic simulation of signal transduction system in hippocampal long-term
potentiation with dynamic modeling of protein phosphatase 2A
Shinichi Kikuchi1, Kenji Fujimoto1, Noriyuki Kitagawa1, Taro Fuchikawa1, Michiko Abe1,
Kotaro Oka1, 2, Kohtaro Takei1, 3, Masaru Tomita1(Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University 1, Dept. of
Biosciences and Informatics, Faculty of Science and Technology, Keio University2, Dept. of
Molecular Pharmacology and Neurobiology, Yokohama City University School of Medicine3)

505

Assessment of Intestinal First Pass Effect by TMF Model: A Study on
Metoprolol, CYP2D6 Substrate

Takashi Mizuma1, Masahiro Hayashi1(Tokyo University of Pharmacy and Life Science 1)

506

Structural Search with Pharmacological Information in 3D
Pharmaceutical Structure Database (3DPSD)
Manabu Watanabe1, Kaori Kurata1, Masaki Hamada1, and Akira Dobashi1(Tokyo University of Pharmacy and Life Science, School of Pharmacy1)

507

Research on Construction and Practical Use of Pediatric Dosage Database
System which Assists Prescribing and Inspection
Masaharu Terasawa1 Mitsuhiro Okazaki2 Miki Kaneuchi2 Hiromichi Yukawa3 Noriaki
Tamura3 Yoshiyuki Kosugi1 Naonori Kohri2 Yukitoshi Hayase2 Tatsuo Nagasaka1(Tokyo University of Pharmacy and Life Science1 Hokkaido College of Pharmacy2 JR East
Japan Information Systems Company3)

508

Data Evaluation and Investigation for Ames Mutagenicity Prediction and
QSAR Analysis: Trend Analysis by Lipinski Parameters and Chemical
Parameters
Katsuhiko Sawatari1, Yoshifumi Nakanishi1, Kohtarou Yuta2, Taijiro Matsushima3(National Institute of Industrial Health1, Fujitsu Ltd.2, Japan Bioassay Research Center3)

6. 疾病モデル
601

DRY WET Hybrid Supporting System for Genomic Translational
Research (Hybrid-TRS)
Jun Nakaya1, Akira Sasaki1, Hideji Ohtani2, Reiko Tachino3, Takako Sakamoto1, Tetsuo(Institute of Medical Science of the Tokyo University 1, Fujitsu2, Tokyo Clinical ResearchCenter 3)

602

Knowledge Architecture for Bridging Genomic Science and Clinical
Medicine (KAB)
Jun Nakaya1, Koji Sasaki2, Akira Sasaki1, Takako Sakamoto1, Tsuguchika Kaminuma3, Tetsuo
Shimizu1(Institute of Medical Science of the University of Tokyo 1, AdIn Research Inc.2, Biodynamics
Inc. 3)603

Evidence Based Knowledge Structure for Complimentary and Alternative
Medicine (EBKS-CAM)
Jun Nakaya1, Yoshinori Ohtsuka2, Yuko Agishi3, Koji Sasaki4, Tsuguchika Kaminuma5, Tetsuo
Shimizu1(Institute of Medical Science of the University of Tokyo 1, Hokkaido University2, Health andResort Research Institute 3, AdIn Research Inc.4, Biodynamics Inc.5)604Functional Analysis of Mammalian Cell Cycle Using a Computational
Model of Hybrid Petri Net
Shuji Kotani 1 , Takashi Yoshioka 2 , Kaoru Takahashi 1 , Akihiko Konagaya 1(RIKEN Genomic Sciences Center (GSC) 1, NTT DATA Corporation 2)

605

Molecular Knowledge Base for Syndrome X
Tsuguchika Kaminuma1, Masumi Yukawa2, Naomi Komiyama2, Hiroki Momose3, Yoshitomo
Tanaka3, Hiroshi Tanaka3(Biodynamics Inc.1, Chem-Bio Informatics Society2, Medical Research Institute, Tokyo
Medical and Dental University3)

606

An Electrophysiological Simulation Model of the Myocardial Cell Using ECELL System
Sayaka Ishinabe 1,2, Yasuhiro Naito 1,3, Motohiro Yoneda 1,2, Katsuya Kawai 1,2, Shoko
Miyamoto 1,2, Shinobu Kuratomi 4, Nobuaki Sarai 4, Satoru Matsuoka 4, Akinori Noma 4, Masaru
Tomita 1,3(Institute for Advanced Biosciences, Keio University 1, Graduate School of Media andGovernance, Keio University2, Department of Environmental Information, Keio University 3,
Department of Physiology and Biophysics, Graduate School of Medicine, Kyoto University 4)

7. その他―新規技術
701

Methylation profile of CpG islands in promoter region for the genes
related pancreatic carcinogenesis
Takazumi Kozaki1, 4, Johji Imura2, Haruo Iguchi3, Aki Hasegawa1, Masafumi Yohda4 and Ryuji
Kawaguchi1(Genomics Research Institute, SRL, Inc1, Department of Surgical and Molecular Pathology,
Dokkyo University of School of Medicine 2, Department of Clinical Research, National Kyusyu
Cancer Center3, Department of Biotechnology and Life Science, Tokyo University ofAgriculture and Technology4)702Development of a new detection device for micro-beads using optical fibers
Kazumi Sawakami1, Hatsumi Abe1, Osamu Segawa1, Masaaki Takahashi1, Hideji Tajima1, Ken
Tsukii2, Toru Takahashi2, Xu Jie2, Sadayuki Toda3, Masayuki Machida4(Precision System Science Co., Ltd.1, The Furukawa Electric Co., LTD.2, FI-Techno Co., Ltd.3,
AIST RCG4)

703

Hierarchical Stratification of Protein Protein Interaction Network
Takeshi Hase, Yasuhiro Suzuki, Souichi Ogishima, Sou Nakagawa, Hiroshi Tanaka(Dept. of Bioinformatics, Graduate School of Tokyo Medical and Dental University)704

An efficient way to perform DDBJ homology search
Takashi Miyajima1, Yutaka Kawarabayasi2(TM Software, Inc.1, AIST2)

705

Expression and characterization of an extracellular molecular chaperone,
Clusterin
Yuko Arie, Nobuo Misawa, Ryo Iizuka, and Masafumi Yohda(Dept. of Biotechnol., Tokyo Univ. of Agric. & Technol.)706

Structure and function of Hsp42 from Saccharomyces cerevisiae
Maya Hirose1, Keisuke Usui1, Nriyuki Ishii2, Masafumi Yohda1(Tokyo University of Agriculture and Technology 1, Nat. Inst. of Adv. Ind. Sci. and Tech 2)707

Effect of ATP binding on the conformation of archaeal group II
chaperonin
Ryo IIZUKA1, Takao YOSHIDA2, Yasuhito SHOMURA3, Kunio MIKI3, Tadashi
MARUYAMA4, Tomonao INOBE5, Kunihiro KUWAJIMA 5, Masafumi YOHDA1(1Dept. of Biotechnol., Tokyo Univ. of Agric. & Technol., 2Inst. for Frontier Medical Sciences,
Kyoto Univ., 3Dept. of Chemistry, Grad. School of Science, Kyoto Univ., 4Japan Marine
Science & Technology Center, 5Dept. of Physics, Grad. School of Science, Univ. of Tokyo)

708

Structural & functional characterization of ClpC from Bacillus subtilis
Keisuke UCHIDA1, Ryo IIZUKA1, Noriyuki ISHII2, Masafumi YOHDA1(1Dept. of Biotechnol., Tokyo Univ. of Agric. & Technol., 2JBIRC, AIST)

709

Development of the Total System for Molecular Design
Tetsuhiro Suzukawa, Soichiro Mizobuchi, Masamoto Arakawa, Kimito Funatsu(Toyohashi University of Technology)

710

Development of a molecular memory system based on hairpin DNA
Masahiro Takinoue1, Akira Suyama1, 2(Institute of Physics University of Tokyo1, JST CREST2)711

SYCRP1-DNA binding mechanism studied through thermodynamic andstructural data.
Katsumi Omagari1 , Hidehisa Yoshimura1, Mitsunori Takano1 , Masayuki Ohmori1, Akinori
Sarai2, Akira Suyama1(Univ. of Tokyo1, Kyushu Inst. of Tech.2)

712

Roles of the helical protrusion of the group II chaperonin
So Sena1, Ryo Iizuka1, Tomonao Inobe2, Kunihiro Kuwajima2, Masafumi Yohda1(Tokyo University of Agriculture and Technology 1, Tokyo University2)

713

Development of Bio-Strand System for multiple samples/items analysis
Yukiko Miyashita1, Junko Asahina1, Osamu Segawa1, Yuriko Tojo1, Masaaki Takahashi1,
Hideji Tajima1, Masafumi Yohda2(Precision System Science Co., Ltd.1, Tokyo University of Agriculture and Technology 2)

714

Development of SNPs detection method using MagSNiPer
Fumiko Kakihara1, 2, Akiko Katsura1, Junichi Akutsu1, Mina Okochi1, Yuriko Tojo3, Hideji
Tajima 3, Masafumi Yohda1, Setsuo Hasegawa2(Tokyo University of Agriculture and Technology 1, Sekino Clinical Pharmacology Clinic2,
Precision System Science3)

715

Fluorescence detection and kinetic analysis of interaction between
Pyrococcus prefoldin and substrate
Tamotsu Zako1, Ryo Iizuka2, Mina Okochi2, Taro Ueno1, Masafumi Yohda2, Takashi Funatsu1(Waseda University1, Tokyo University of Agriculture and Technology 2)

716

OBIGrid application of Blast service in the hetero cluster of parallel
Fumikazu KONISHI1, Ryo UMETSU1, Akihiko KONAGAYA 1(RIKEN Genomic Sciences Center1)

717

Complex dissociation and the role of N-terminal region of sHsp from
Sulfolobus tokodaii strain 7
Keisuke Usui1, Omer Faruk Hatipoglu1, Noriyuki Ishii2, Masafumi Yohda1(Tokyo University of Agriculture and Technology 1, National Institute of Advanced Industrial
Science and Technology 2)

718

Simulation of apoptosis based on the labeling problem
Akira Tachikawa(Department of Biomedical Engineering, Graduate School of Medicine, University of Tokyo)

719

Application of Drug Interaction Ontology (DIO) for Possible Drug-drugInteractions
Sumi Yoshikawa 1, 2, Kenji Satou 1, Akihiko Konagaya2(School of Knowledge Science, Japan Advanced Institute of Science and Technology (JAIST) 1,
Genomics Science Center (GSC), RIKEN (The Institute of Physical and Chemical Research) 2)

720

Comprehensive analysis of yeast DNA-binding proteins by phage display
and DNA microarray
Hiroko Hagiwara1, Sumiko Kunihiro1, Midori Yamamoto1, Keiichi Nakajima1, Motoaki Sano1,
Kumiko Takase1, Haruhiko Masaki2, Ichiro Kuwabara3, Ichiro Maruyama3, Masayuki Machida1(1AIST, 2Univ. of the Tokyo, 3The Scripps Res. Inst.)

721

A Discrete Mathematical Model of Inflammatory Response
Yasuhiro Suzuki1,2, Michihiko Koeda1, Hiroshi Tanaka1(Tokyo Medical and Dental University1, Advanced Telecommunications Research inst.2)