Refereed Articles

K. Fukui, K. Takahashi, "Infrared multiple photon dissociation Spectroscopy and Computational Studies of O-Glycosylated Peptides.", Analytical Chemistry, 84, 2188-2194 (2012)

S. Yamasaki, S. Nakamura, K. Fukui, "Prospects for tertiary structure prediction of RNA based on secondary structure information." Journal of Chemical Information and Modeling, 52, 557-67 (2012)

M. M. Gromiha, M. Swadamini, K. Fukui, "Structure-Function Relationship in Olfactory Receptors." Lecture Notes in Bioinformatics, 6840, 618-623 (2011)

M. M. Gromiha, K. Fukui, "Scoring Function Based Approach for Locating Binding Sites and Understanding Recognition Mechanism of Protein-DNA Complexes." Journal of Chemical Information and Modeling, 51, 721-729 (2011)

W. Nemoto, K. Fukui, H. Toh, "GRIPDB - G protein coupled Receptor Interaction Partners DataBase." Journal of Receptors and Signal Transduction, 31, 199-205 (2011)

M. M. Gromiha, K. Yokota, K. Fukui, "Sequence and structural analysis of binding site residues in protein-protein complexes." International Journal of Biological Macromolecules, 46, 187-192 (2010)

M. M. Gromiha, S. Selvaraj, B. Jayaram, K. Fukui, "Sequence and Structural features of binding site residues in protein-protein complexes." PROTEOME SCIENCE, 9-Suppl 1, 1-6 (2010)

M. M. Gromiha, S. Selvaraj, B. Jayaram, K. Fukui, "Identification and Analysis of Binding Site Residues in Protein Complexes: Energy Based Approach." Advanced Intelligent Computing Theories and Applications, 6215, 626-633 (2010)

M. Michael Gromiha, K. Yokota and K. Fukui, Understanding the recognition mechanism of protein-RNA complexes using energy based approach. Curr. Protein Peptide Sci. 11, 629-638 (2010)

M. Michael Gromiha, K. Yokota and K. Fukui, Sequence and structural analysis of binding site residues in protein-protein complexes. Int. J. Biol. Macromol. 46, 187-192 (2010)

M. Michael Gromiha, S. Selvaraj, B. Jayaram and K. Fukui, Identification and analysis of binding site residues in protein complexes: energy based approach. Lecture Notes in Comp. Sci. 6215, 626-633 (2010)

M. Michael Gromiha, Y. Yabuki, M.X. Suresh, A.M. Thangakani, M. Suwa and K. Fukui TMFunction: database for functional residues in membrane proteins. Nucleic Acids Res 37, D201-204 (2009)

M. Michael Gromiha, Kiyonobu Yokota and Kazuhiko Fukui, "Identification and analysis of binding site residues in protein-protein complexes", Proc. World Academy of Sciene and Technology, 57, pp.127-132 (2009)

W. Nemoto, K. Fukui, H. Toh, "GRIP: A server for predicting interfaces for GPCR oligomerization." Journal of Receptors and Signal Transduction, 29, 312-317 (2009)

M. Michael Gromiha, Kiyonobu Yokota and Kazuhiko Fukui, "Energy based approach for understanding the recognition mechanism in protein?protein complexes." Mol. BioSyst., 5, 1779-1786 (2009)

T. Yoshikawa, K. Tsukamoto, Y. Hourai, K. Fukui, "Improving the Accuracy of an Affinity Prediction Method by Using Statistics on Shape Complementarity between Proteins." Journal of Chemical Information and Modeling, 49, 693-703 (2009)

K. Tsukamoto, T. Yoshikawa, Y. Hourai, K. Fukui, "The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning." Computational Biology and Chemistry: Advances and Applications, 2, 1-15 (2009)

H. Suzuki, A. Kameyarna, K. Tachibana, H. Narimatsu, K. Fukui, "Computationally and Experimentally Derived General Rules for Fragmentation of Various Glycosyl Bonds in Sodium Adduct Oligosaccharides." Analytical Chemistry, 81, 1108-1120 (2009)

M. M. Gromiha, Y. Yabuki, M. X. Suresh, A. M. Thangakani, M. Suwa, K. Fukui, "TMFunction: database for functional residues in membrane proteins." Nucleic Acids Research, 37, D201-D204 (2009)

T. Yoshikawa, K. Tsukamoto, Y. Hourai, K. Fukui, "Parameter tuning and evaluation of an affinity prediction using protein-protein docking." Mmactee' 08: Proceedings of the 10th Wseas International Conference Mathermatical Methods and Computational Techniques in Electrical Engineering, 312-317 (2008).

K. Tsukamoto, T. Yoshikawa, Y. Hourai, K. Fukui, Y. Akiyama, "Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins." J. Bioinform Comput Biol, 6, 1133-56 (2008).

K. Tsukamoto, K. Fukui, "Bio-scale Engine: Reaction Mechanism of Nitric Oxide Reductase Cytochrome P450nor from Fusarium oxysporum." Proceedings of the 12th Wseas International Conference on Computers, Pts 1-3, 452-457 (2008).

H. Suzuki, T. Yamagaki, K. Tachibana, K. Fukui, "Fragmentation of Lewis-type trisaccharides in the gas phase: Experimental and theoretical studies." International Journal of Mass Spectrometry, 278, 1-9 (2008).

K. Fukui, Y. Takada, H. Sumiyoshi, H. Imai, K. Takahashi, "IRMPD Spectroscopic Analysis of Peptides and Oligosaccharides by Using FTICR MS with a Mid-Infrared Free-Electron Laser", J. Phys. Chem. B, 110, 16111-16116 (2006).

K. Fukui, Y. Akiyama, K. Takahashi, "Fragmentation Studies of Peptide and Oligosaccharide using a Mid-IR Free Electron Laser", Japan Society for Laser Surgery and Medicine, 27, 92-96 (2006)

K. Fukui, A. Kameyama, Y. Mukai, K. Takahashi, N. Ikeda, Y. Akiyama, H. Narimatsu, H., "A computational study of the structure-reactivity relationships in Na-adduct oligosaccharides in the collision-induced dissociation reactions", Carbohydr. Res., 341, 624-633 (2006)

T. Yamagaki, K. Fukui, K. Tachibana, "Analysis of glycosyl bond cleavage and related isotope effects in collision-induced dissociation quadrupole/time-of-flight mass spectrometry of isomeric trehaloses", Anal. Chem. 78,1015-1022 (2006)

K. Fukui, Y. Akiyama, K. Takahashi, "Fragmentation study of peptides using FTICR with infrared multiplephoton dissociation:experiment and simulation",Eur. J. Mass Spectrom., 10, 639-648 (2004)

K. Fukui, Y. Akiyama, K. Takahashi, "Charge-state selective fragmentation analysis for protonated peptides in infrared multiplephoto dissociation",Int. J. Mass Spectrom., 235, 25-32 (2004)

A. Suenaga, M. Hatakeyama, M. Ichikawa, X. Yu, N. Futatsugi, T. Narumi, K. Fukui, T. Terada, M. Taiji, M. Shirouzu, S. Yokoyama, A. Konagaya, "Molecular dynamics, free energy, and SPR analyses of the interactions.between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides", Biochemistry, 42, 5195-5200 (2003)

K. Fukui, B. G. Sumpter, C. Yang, D. W. Noid, and R. E. Tuzun "Analysis of.Eigenvalues and Eigenvectors of Polymer Particles: Random Normal Modes" Comput. Theor. Polym. Sci. 11, 191 (2001)

K. Fukui, B. G. Sumpter, C. Yang, D. W. Noid, and R. E. Tuzun, "Large-Scale Normal Coordinate Analysis of Macromolecular Systems: Thermal Properties of Polymer Particles and Crystals", J. Phys. Chem. B 104, 526 (2000)

K. Fukui, B. G. Sumpter, C. Yang, D. W. Noid, and R. E. Tuzun, "Spectra Analysis for Macromolecular System: Chain Length Effects in Polymer Particles", J. Polym. Sci. Part B: Polymer Physics, 38, 1812 (2000)

K. Fukui, B. G. Sumpter, M. D. Barnes, and D. W. Noid,"Atomistic dynamics of nano-scale polymer particles", Macromolecules 33, 5982 (2000)

C. Yang, K. Fukui, B. G. Sumpter, D.W. Noid, and R. E. Tuzun, "Computing the density of states for large-scale polymer systems" Macromol. Theory Simul. 9, 428-432 (2000)

B. G. Sumpter, K. Fukui, M. D. Barnes and D. W. Noid,"Computational Simulation and Modeling of Polymer-Composite Nanoparticles:.New Insights and Directions for Advanced Materials", Materials Today 2, 3-6.(2000)

D. W. Noid, K. Fukui, B. G. Sumpter, C. Yang and R.E. Tuzun, "Time Averaged Normal Coordinate Analysis of Polymer Particles and Crystals", Chem. Phys. Lett. 316, 285 (2000)

K. Fukui, B. G. Sumpter, M. D. Barnes, D. W. Noid, and J. U. Otaigbe,"Molecular Dynamics Simulation of the Thermal Properties of Nano-Scale Polymer Particles", Macromol. Theory Simulat. 8, 38 (1999)

M. D. Barnes, C.-Y. Kung, N. Lermer, K. Fukui, B. G. Sumpter, and D. W. Noid, "A Homogeneous polymer blend microparticles with a tunable refractive index", Opt. Lett. 24, 121 (1999)

K. Fukui, B. G. Sumpter, M. D. Barnes, and D. W. Noid, "Molecular Dynamics Studies of the Structure and Properties of Polymer Nano-Particles", Comput. Theor. Polym. Sci. 9, 245 (1999)

K. Fukui, B. G. Sumpter, K. Runge, C. Kung, M. D. Barnes, and D. W. Noid, "Collision Dynamics of Nano- Scale Polymer Particles on Surfaces", Chem. Phys. 244, 339 (1999)

M. D. Barnes, K. C. Ng, K. Fukui, B. G. Sumpter, and D. W. Noid, "Polymer-blend Microparticles: A New Approach to Nanoscale Composites with Tunable Properties", Materials Today 2, 25 (1999)

K. Fukui, B. G. Sumpter, M. D. Barnes, and D. W. Noid, "Molecular Dynamics Simulation of Polymer Fine Particles: Physical and Mechanical Properties", Polym. J. 31 664 (1999)

M. D. Barnes, K. C. Ng, K. Fukui, B. G. Sumpter, and D. W. Noid, "Probing Phase-Separation Behavior in Polymer-Blend Microparticles: Effects of Particle Size and Polymer Mobility", Macromolecule, 32, 7183 (1999)

K. Fukui, J. H. Frederick and J. I. Cline, "Chiral Dissociation Dynamics of Molecular Ratchets: Preferential Senses of Rotary Motion in Microscopic Systems", Phys. Rev. A. 58, 929 (1998)

K. Fukui, B. G. Sumpter, D. W. Noid, and J. U. Otaigbe, "Atomistic Simulation and Modeling of Ultra Fine Polymer Particles", Polymer Preprints (ACS, Div. Polym. Chem.) 39, 612 (1998).

K. Fukui, J. I. Cline and J. H. Frederick, "Canonical Sampling of classical phase space: Application to molecular-vibration dynamics", J. Chem. Phys. 107, 4551 (1997)

K. Fukui, J. H. Frederick and J. I. Cline, "Classical Trajectory Study of Product State Vector Correlations : A Model for the Photodissociation of CF3NO", J. Chem. Phys. 107, 4564 (1997)

Conference Proceedings

Fukui K, Takahashi K, "Photodissociation study of Peptides and Oligosaccharides by Infrared Spectroscopy using FTMS-FEL-SUT", Conference Proceedings, 54th ASMS Conference on Mass Spectrometry (2006)

Fukui,K., Akiyama,Y., Takahashi,K. :"Fragmentation studies for peptides using FTICR mass spectrometry and MS/MS: Experiment and simulation", 224th American Chemical Society (ACS) National Meeting (Boston, MA, USA) (Aug. 2002) (ポスター発表).

Kameyama A , Fukui K, Nakaya S, Ito H, Sukegawa M, Narimatsu H,"Empirical Rules for Fragmentations of Oligosaccharides during Low-Energy CID in MALDI QIT-TOF Mass Spectrometer" Conference Proceedings, 54th ASMS Conference on Mass Spectrometry (2006)

Fukui K, Kameyama A, Mukai Y, Takahashi K, Akiyama Y, Narimatsu H, "Computationa l study of structure-reactivity for Na adduct oligosaccharides" Abstracts of Pap ers of The American Chemical Society 230: U688-U689 74-CARB (2005)

Kumondai K, Fukui K, Takada Y, Terasaki M, Takahashi K "Photodissociation study of protonated peptides in FTICR mass spectrometry" Abstracts of Papers of The Am erican Chemical Society 230: U2939-U2939 360-PHYS (2005)

K. Fukui, Y. Akiyama, "Exhausive computational analysis of peptides for the frag mentation in low-energy dissociation mass spectrometry" Abstracts of Papers of T he American Chemical Society 230: U1359-U1360 227-COMP (2005)

K. Fukui, Y. Akiyama, K. Takahashi, Tohru Yamagaki, "Theoretical and experimenta l studies for isomers of oligosaccharides using CID-MS/MS quadropole/time-of-fli ght mass spectrometry", Abstracts of Papers of The American Chemical Society 228 : U230-U230 074-CARB Part 1 (2004)

Fukui,K., Akiyama,Y., Naito,Y., Takahashi,K. :"ESI-FTICR MS with Infrared Multiphoton Dissociation :Analysis of Fragmentation of Peptides", 50th Annual Conference American Society for Mass Spectrometry (ASMS) (2002).

福井 一彦 :"ペプチド切断の質量分析計による解析", AIST Today, 10月号 p.15 (2002).

福井 一彦 :"レーザー誘起化学反応によるポリペプチド切断", 産総研 生命情報科学人材養成コース設立1周年記念シンポジウム (お台場・東京) (2002. 10).

福井 一彦, 内藤 康秀, 秋山 泰, 高橋 勝利 :"衝突誘起解離や赤外多光子解離によるm/z選択的ペプチド切断解析", 産総研 生命情報科学人材養成コース設立1周年記念シンポジウム (お台場・東京) (2002. 10) (ポスター発表).

福井 一彦, 内藤 康秀, 秋山 泰, 高橋 勝利 :"衝突誘起解離や赤外多光子解離を使ったペプチド切断の実験・理論", 3rd Annual Meeting of Chem-Bio Informatics Society (CBI) (東京) (2002. 9).

Patent

JP Ap.No.2002-153559. Method for Predicting Bond Cleavages in Excited Polypeptides (3829186 2006/07/21)

JP Ap.No.2002-347786 Protein-induced Dissociation Device and Method for Bio-polymer Molecules (3928043 2007/03/16)

JP Ap.No. 2004-120804 Apparatus for analyzing polymer and method of polymer analysis

JP Ap.No. 2004-240845 Apparatus of fragment pattern analysis for Oligosaccharides and method of the pattern analysis