Seibutsu Butsuri

Volume 43, Issue supplement

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Plasticity in protein folding

M. Arai

Article type: Article
2003Volume 43Issue supplement Pages S24-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S24_2

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Minimum information required for constructing a native protein structure

Y. Kuroda

Article type: Article
2003Volume 43Issue supplement Pages S24-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S24_3

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Roles of Hydrophobic-Core Residues in Protein Folding

K. Tsugika, Ismail.E Rozi, Y. Seki, M. Jin, K. Mori, K. Soda

Article type: Article
2003Volume 43Issue supplement Pages S25-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S25_1

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On Problems in Defining Hydrogen Bonds of Protein Interior

T. Hsra, Y. Seki, K. Soda

Article type: Article
2003Volume 43Issue supplement Pages S25-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S25_2

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Clustering of Fluorinated Alcohols and Their Preferential Interaction with Proteins

T. Tomizawa, Y. Seki, A. Kato, K. Soda

Article type: Article
2003Volume 43Issue supplement Pages S25-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S25_3

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Molecular dynamics study of a protein-inhibitor association

H. Miyagawa, K. Kitamura

Article type: Article
2003Volume 43Issue supplement Pages S25-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S25_4

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Dielectric property of Alkali-Halide salts with hydration shells in water

Umme Salmal Nazia, Syed Rashel Kabir, Y. Furihata, T. Kodama, M. Suzuk ...

Article type: Article
2003Volume 43Issue supplement Pages S26-
Published: August 25, 2003
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DOIhttps://doi.org/10.2142/biophys.43.S26_1

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Dielectric property of Globular Protein with hydration shells in water

T. Miyazaki, K. Yokoyama, T. Kamei, M. Suzuki

Article type: Article
2003Volume 43Issue supplement Pages S26-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S26_2

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Quantum chemical study on the in silico prediction of protein functions.

K. Fukushima, Mituhito M., Y. Inoue, M. Sakurai

Article type: Article
2003Volume 43Issue supplement Pages S26-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S26_3

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A theoretical study of Electron transfer in protein : Influence of protein dynamics and hydrogen bonds

C. Kobayashi, Kim Baldridge, Jose Onuchic

Article type: Article
2003Volume 43Issue supplement Pages S26-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S26_4

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Neutron crystallography of B-DNA decamer d(CCATTAATGG)

S. Arai, T. Chatake, K. Kurihara, I. Tanaka, T. Ohhara, N. Niimura

Article type: Article
2003Volume 43Issue supplement Pages S27-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S27_1

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Unique quadruplex structure of GGA triplet repeat DNA and its biological significance

A. Matsugami, K. Ouhashi, T. Okuizumi, T. Ikeda, H. Sotoya, S. Uesugi, ...

Article type: Article
2003Volume 43Issue supplement Pages S27-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S27_2

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Molecular dynamics simulation of RuvA and Holliday junction DNA Complex

H. Ishida, N. Go

Article type: Article
2003Volume 43Issue supplement Pages S27-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S27_3

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Layered Structure of Xenopus laevis Sperm Chromatin Probed by Nanomechanical Method

Faezeh Mahichi, K. Ohsumi, H. Arakawa, Rehana Afrin, A. Ikai

Article type: Article
2003Volume 43Issue supplement Pages S27-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S27_4

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Semi-flexible Polyelectrolyte in Poor Solvent : A possibility of intra-chain segregation

T. Sakaue, N. Miyazawa

Article type: Article
2003Volume 43Issue supplement Pages S28-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S28_2

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Salt inhibits polyamine-induced compaction of giant DNA

N. Makita, K. Yoshikawa

Article type: Article
2003Volume 43Issue supplement Pages S28-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S28_3

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Collapsing Transition of DNA and Counter Ion Exchange

Y. Murayama, M. Sano

Article type: Article
2003Volume 43Issue supplement Pages S28-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S28_4

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Metal ion recognition of the metal-binding motif in hammerhead ribozymes

Y. Tanaka, Y. Kasai, C. Kojima, K. Yamasaki, H. Morita, K. Taira

Article type: Article
2003Volume 43Issue supplement Pages S28-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S28_5

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Switching of transcriptional activity caused by discrete transition on the higher order structure of DNA

A. Yamada, K. Kubo, N. Makita, K. Yoshikawa

Article type: Article
2003Volume 43Issue supplement Pages S29-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S29_1

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Folding transition of a large DNA molecule causes ON/OFF switching of its transcriptional activity

K. Tsumoto, Francois Luckel

Article type: Article
2003Volume 43Issue supplement Pages S29-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S29_2

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A study of the effects of metal ion and solvent on the DNA replication from the viewpoint of liquid phase cluster

S. Mochizuki, A. Wakisaka

Article type: Article
2003Volume 43Issue supplement Pages S29-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S29_3

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Thermodynamic Database for Protein-Nucleic Acid Interactions(ProNIT) : Recent Developments

Shaji Kumar, Ponraj Prabakaran, H. Uedaira, Michael Gromiha, K. Kitaji ...

Article type: Article
2003Volume 43Issue supplement Pages S29-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S29_4

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Recognition of base sequence by amino acid side chain : interaction free energy landscape and its dependence on sequence context

T. Yoshida, M. Aida, A. Sarai, M.Michael Gromiha

Article type: Article
2003Volume 43Issue supplement Pages S30-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S30_1

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cAMP receptor protein-DNA binding mechanism inferred from free energy changes due to systematic base pair substitution

K. Omagari, H. Yoshimura, M. Takano, Hao Dongyun, M. Ohmori, A. Sarai, ...

Article type: Article
2003Volume 43Issue supplement Pages S30-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S30_2

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Energy analysis of E. coli tRNA^<Gln> and its aptamer complexed with GlnRS by Molecular dynamics simulation

S. Yamasaki, S. Nakamura, T. Terada, K. Shimizu

Article type: Article
2003Volume 43Issue supplement Pages S30-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S30_3

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QSAR analysis of protein-DNA complexes

A. Sarai, Ponraj Prabakaran, Joerg Siebers, Shandar Ahmad, Michael Gro ...

Article type: Article
2003Volume 43Issue supplement Pages S30-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S30_4

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Visualization of topoisomeraze I and supercoiled DNA by atomic force microscopy

Y. Chiyoda, Y. Wada, W. Hiraoka

Article type: Article
2003Volume 43Issue supplement Pages S31-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S31_2

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Monoclonal antibody which distinguishes the length of DNA

Y. Hanyu, M. Kato, Y. Onishi

Article type: Article
2003Volume 43Issue supplement Pages S31-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S31_3

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Automatic evaluation of the topological similarity of protein structures

I.Ekoprayitno Rozi, Y. Yamada, K. Tsugika, K. Soda

Article type: Article
2003Volume 43Issue supplement Pages S31-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S31_4

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Precise reevaluation of the atomic packing density of protein

Y. Yamada, Y. Seki, I.Ekoprayitno Rozi, K. Soda

Article type: Article
2003Volume 43Issue supplement Pages S31-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S31_5

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Development of a fragment library for solvent accessibility prediction and comparison with neural network approach

Shandar Ahmad, Michael Gromiha, Akinori Sarai, J.-Y. Wang

Article type: Article
2003Volume 43Issue supplement Pages S32-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S32_2

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Optimization of force field parameters for protein systems by the PDB database

Y. Sakae, Y. Okamoto

Article type: Article
2003Volume 43Issue supplement Pages S32-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S32_3

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Differences in the Folding Kinetics of Lysozyme Family by Contact Maps Based on the Interresidue Average Distance Statistics

S. Nakajima, T. Kikuchi

Article type: Article
2003Volume 43Issue supplement Pages S32-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S32_4

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Analysis of beta-Barrel Protein Structures by Contact Maps Based on the Interresidue Average Distance Statistics

Y. Ishizuka, T. Kikuchi

Article type: Article
2003Volume 43Issue supplement Pages S32-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S32_5

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Analysis of Folding of Ribosomal S6 and its Circular Permutant by Contact Maps Based on the Interresidue Average Distance Statistics

T. Okada, T. Kikuchi

Article type: Article
2003Volume 43Issue supplement Pages S33-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S33_2

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Development of energy minimization algorithm considering solvation effect in dihedral angle space

T. Takahashi, S. Endo, H. Wako

Article type: Article
2003Volume 43Issue supplement Pages S33-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S33_3

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Simulating 3D structure of Membrane Proteins

T. Miki, Y. Fujitsuka, S. Takada

Article type: Article
2003Volume 43Issue supplement Pages S33-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S33_4

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Application of ab initio prediction of protein structures

T. Nishimura, S. Nakamura, K. Shimizu

Article type: Article
2003Volume 43Issue supplement Pages S33-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S33_5

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De novo protein tertiary strucuture prediction : Improvement of prediction using variable fragment

T. Ishida, S. Nakamura, K. Shimizu

Article type: Article
2003Volume 43Issue supplement Pages S34-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S34_1

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Replicaexchange molecular dynamic simulations performed in the vicinity of the native structure of a protein

T. Nagasima, T. Mitsui, A. Kinjo, K. Nishikawa

Article type: Article
2003Volume 43Issue supplement Pages S34-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S34_2

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An analysis of conformational change of a protein upon binding to ligand by multicanonical MD

T. Terada, S. Nakamura, K. Shimizu

Article type: Article
2003Volume 43Issue supplement Pages S34-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S34_3

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Flexible docking molecular dynamic simulation between enzyme and inhibitor

N. Kamiya, J. Higo

Article type: Article
2003Volume 43Issue supplement Pages S34-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S34_4

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Analysis of interactions between cellobiose dehydrogenase and substrates by molecular dynamics simulation

K. Hibi, T. Terada, S. Nakamura, K. Igarashi, M. Kitaoka, K. Shimizu

Article type: Article
2003Volume 43Issue supplement Pages S35-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S35_1

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A quantum chemical method for rapid optimization of protein structures

M. Wada

Article type: Article
2003Volume 43Issue supplement Pages S35-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S35_2

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Comparison of free-energy profiles of small peptides between the generalized Born and the explicit solvent models

T. Ishizuka, T. Terada, S. Nakamura, K. Shimizu

Article type: Article
2003Volume 43Issue supplement Pages S35-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S35_3

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Development of ProMode and analysis of dynamic domains

H. Wako, M. Kato, S. Endo

Article type: Article
2003Volume 43Issue supplement Pages S35-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S35_4

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X-ray crystal structure analysis of Oligoxyloglucan reducing end-specific cellobiohydrolase

H. Kondo, K. Yaoi, M. Suzuki, N. Noro, S. Tsuda, Y. Mitsuishi

Article type: Article
2003Volume 43Issue supplement Pages S36-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S36_1

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Analysis of substrate binding site of metallo-beta-lactamase(IMP-1) produced by drug resistant bacteria means of X-ray crystallography.

Y. Yamaguchi, H. Kurosaki, Y. Yamagata, Y. Arakawa, M. Goto

Article type: Article
2003Volume 43Issue supplement Pages S36-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S36_2

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Study on protein-protein interaction between barnase and barstar on the basis of their hydration structures

T. ikura

Article type: Article
2003Volume 43Issue supplement Pages S36-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S36_3

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The crystal structure of the mutant of conger eel galectin, congerinII with increased Thermostability

C. Shionyu, Y. Miwa, T. Shirai, T. Yamane, Y. Ito, T. Ogawa, K. Muramo ...

Article type: Article
2003Volume 43Issue supplement Pages S36-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S36_4

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