Seibutsu Butsuri

Volume 43, Issue supplement

Displaying 201-250 of 1005 articles from this issue

Download citation

Show all abstracts

Multiple conformations of activated Ras observed directly by single molecule FRET

Y. Arai, T. Wazawa, H. Yokota, A.H. Iwane, Y. Ishii, Kataoka Kataoka, ...

Article type: Article
2003Volume 43Issue supplement Pages S49-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S49_3

JOURNAL FREE ACCESS

Download PDF (265K)
Molecular dynamics simulation of outer membrane channel protein, maltoporin of E.coli

K. Seki, A. Suenaga, T. Narumi, M. Taiji, C. Danelon, M. Winterhaulter ...

Article type: Article
2003Volume 43Issue supplement Pages S49-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S49_4

JOURNAL FREE ACCESS

Download PDF (265K)
Prediction of DNA binding surface of proteins, by evaluating the scores of electrostatic potential and the shape of molecular surface

Y. Tsuchiya, K. Kinoshita, H. Nakamura

Article type: Article
2003Volume 43Issue supplement Pages S50-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S50_1

JOURNAL FREE ACCESS

Download PDF (258K)
Molecular dynamics simulation study of 8-oxo-dGMP recognition mechanism of MutT

M. Higuchi, H. Ishida, A. Kitao, Y. Yamagata, N. Go

Article type: Article
2003Volume 43Issue supplement Pages S50-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S50_2

JOURNAL FREE ACCESS

Download PDF (258K)
Conservation of Native-like Module Structure in Unfolding of Barnase

K. Shinoda, K. Takahashi, M. Go

Article type: Article
2003Volume 43Issue supplement Pages S50-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S50_3

JOURNAL FREE ACCESS

Download PDF (258K)
Quantum Chemical Study of Antibody Affinity Maturation

K. Ohno, Y. Inoue, M. Sakurai

Article type: Article
2003Volume 43Issue supplement Pages S50-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S50_4

JOURNAL FREE ACCESS

Download PDF (258K)
A study on molecular recognition mechanism by analyzing strucral changes between monomer and complexed proteins

M. Kato, H. Wako, K. Kinoshita, A. Kidera

Article type: Article
2003Volume 43Issue supplement Pages S51-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S51_1

JOURNAL FREE ACCESS

Download PDF (253K)
Protein Ligand Interaction Database ProLINT and Its Application to QSAR Analysis

K. Kitajima, Shandar Ahmad, H. Kubodera, S. Sunada, A. Sarai

Article type: Article
2003Volume 43Issue supplement Pages S51-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S51_2

JOURNAL FREE ACCESS

Download PDF (253K)
Finding evolutionary relations beyond superfamilies : Fold-based superfamilies

K. Matsuda, T. Kawabata, K. Kinoshita, T. Nishioka, N. Go

Article type: Article
2003Volume 43Issue supplement Pages S51-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S51_3

JOURNAL FREE ACCESS

Download PDF (253K)
De novo protein structure prediction : Optimization of potential function

Y. Fujitsuka, G. Chikenji, S. Takada

Article type: Article
2003Volume 43Issue supplement Pages S51-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S51_4

JOURNAL FREE ACCESS

Download PDF (253K)
Toward highprecision protein structure modeling : Improving force-field

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

Article type: Article
2003Volume 43Issue supplement Pages S52-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S52_1

JOURNAL FREE ACCESS

Download PDF (206K)
Development and evaluation of the single amino acid potential force field (SAAP force field)

M. Iwaoka, D. Yosida

Article type: Article
2003Volume 43Issue supplement Pages S52-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S52_2

JOURNAL FREE ACCESS

Download PDF (206K)
Analysis of Molecular Force Field for peptide chains by abinitio MO method

H. Matsumoto, Y. Seki, K. Soda

Article type: Article
2003Volume 43Issue supplement Pages S52-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S52_3

JOURNAL FREE ACCESS

Download PDF (206K)
Validation of knowledge-based potential derived from virtual structural database

Y. Yuge, H. Nakamura, M. Takano, A. Suyama

Article type: Article
2003Volume 43Issue supplement Pages S52-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S52_4

JOURNAL FREE ACCESS

Download PDF (206K)
Genetic algorithm refinement of force field parameters for Monte Carlo simulation

T. Meguro, T. Ando, I. Yamato

Article type: Article
2003Volume 43Issue supplement Pages S53-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S53_1

JOURNAL FREE ACCESS

Download PDF (234K)
Influence of force fields and implicit solvation on potential energy surface and dynamics

Y. Koyama, M. Takano, S. Tomoda, A. Suyama

Article type: Article
2003Volume 43Issue supplement Pages S53-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S53_2

JOURNAL FREE ACCESS

Download PDF (234K)
A development of a new method for the ligand-protein docking considering the protein flexibility

R. Tatsumi, Y. Fukunishi, H. Nakamura

Article type: Article
2003Volume 43Issue supplement Pages S53-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S53_3

JOURNAL FREE ACCESS

Download PDF (234K)
The dynamic conformational polymorphism and energy landscape in Ras

S. Ohguchi, T.P. Terada, M. Sasai

Article type: Article
2003Volume 43Issue supplement Pages S53-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S53_4

JOURNAL FREE ACCESS

Download PDF (234K)
Free-energy landscape of a chameleon sequence

J. Higo, K. Ikeda

Article type: Article
2003Volume 43Issue supplement Pages S54-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S54_1

JOURNAL FREE ACCESS

Download PDF (259K)
Hydrogen-bond patterns around a protein investigated by MD simulation

T. Yokomizo, T. Yamazaki, H. Shindo, M. Nakasako, J. Higo

Article type: Article
2003Volume 43Issue supplement Pages S54-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S54_2

JOURNAL FREE ACCESS

Download PDF (259K)
Volume Fluctuation Dynamcs of Lysozyme by Molecular Dynamics Simulation

K. Mori, Y. Seki, K. Soda

Article type: Article
2003Volume 43Issue supplement Pages S54-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S54_3

JOURNAL FREE ACCESS

Download PDF (259K)
Protein dynamics of active site studied by the molecular dynamics simulation.

Atushi T., H. Nakagawa, H. Kamikubo, Y. Joti, A. Kitao, M. Kataoka

Article type: Article
2003Volume 43Issue supplement Pages S54-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S54_4

JOURNAL FREE ACCESS

Download PDF (259K)
Timescale dependent protein dynamics studied by incoherent neutron scattering

H. Nakagawa, Hironari H., I. Tsukushi, T. Kanaya, J.C. Smith, M. Katao ...

Article type: Article
2003Volume 43Issue supplement Pages S55-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S55_1

JOURNAL FREE ACCESS

Download PDF (232K)
Mode Coupling in Large Scale Conformational Change

K. Itoh, M. Sasai

Article type: Article
2003Volume 43Issue supplement Pages S55-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S55_2

JOURNAL FREE ACCESS

Download PDF (232K)
Analysis of the motion of substrate protein in the GroEL cavity using FRET technique

T. Ueno, H. Taguchi, H. Tadakuma, M. Yoshida, T. Funatsu

Article type: Article
2003Volume 43Issue supplement Pages S55-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S55_3

JOURNAL FREE ACCESS

Download PDF (232K)
The role of the conformational fluctuation on the activity of E.Coli ClpB

Y. Tani, N. Tanaka

Article type: Article
2003Volume 43Issue supplement Pages S55-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S55_4

JOURNAL FREE ACCESS

Download PDF (232K)
Study on structural segmentspecific fluctuation of DHFR by mass spectrometry

T. Yamamoto, S. Izumi, K. Gekko

Article type: Article
2003Volume 43Issue supplement Pages S56-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S56_1

JOURNAL FREE ACCESS

Download PDF (233K)
The fragment length and energy landscape in fragment assembly method

G. Chikenji, Y. Fujitsuka, S. Takada

Article type: Article
2003Volume 43Issue supplement Pages S56-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S56_2

JOURNAL FREE ACCESS

Download PDF (233K)
A coarse-grained model for structure prediction of alpha/beta proteins

T.N. Sasaki, M. Sasai

Article type: Article
2003Volume 43Issue supplement Pages S56-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S56_3

JOURNAL FREE ACCESS

Download PDF (233K)
Environment induced secondary structure of proteins : Molecular dynamics : Sampling by replica exchange method

T. Kameda, S. Takada

Article type: Article
2003Volume 43Issue supplement Pages S56-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S56_4

JOURNAL FREE ACCESS

Download PDF (233K)
Inter-residue Interactions in Protein Structures : Applications to Protein Folding and Stability

Michael Gromiha, Samuel Selvaraj

Article type: Article
2003Volume 43Issue supplement Pages S57-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S57_1

JOURNAL FREE ACCESS

Download PDF (235K)
Factors that determine a transient accumulation of an intermediate in a folding simulation with the Janustype Go model

H. Nakamura, M. Takano

Article type: Article
2003Volume 43Issue supplement Pages S57-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S57_2

JOURNAL FREE ACCESS

Download PDF (235K)
The roles and occupancies of native or nonnative contact pairs for protein folding process

H. Abe, H. Wako

Article type: Article
2003Volume 43Issue supplement Pages S57-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S57_3

JOURNAL FREE ACCESS

Download PDF (235K)
Folding Energy Landscape of Two Model Peptides : Brownian Dynamics Simulation with Multiple Time Step Method Approach

Tadashi Ando, Toshiyuki Meguro, Ichiro Yamato

Article type: Article
2003Volume 43Issue supplement Pages S57-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S57_4

JOURNAL FREE ACCESS

Download PDF (235K)
The effect on protein-folding of encapsion and forced-unfolding by chaperonin cage : Molecular dynamics simulations

F. Takagi, S. Takada

Article type: Article
2003Volume 43Issue supplement Pages S58-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S58_1

JOURNAL FREE ACCESS

Download PDF (238K)
Protein folding by the effect of macromolecular crowding

S. Negi, N. Tokuriki, M. Kinjo, I. Urabe, T. Yomo

Article type: Article
2003Volume 43Issue supplement Pages S58-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S58_2

JOURNAL FREE ACCESS

Download PDF (238K)
HD-Exchange Reactions of 2SS-Variants of Lysozyme and Implications for the Initial Stage of Folding

K. Sakamoto, K. Yamasaki, Y. Azuma, Y. Noda, H. Tachibana, S. Segawa

Article type: Article
2003Volume 43Issue supplement Pages S58-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S58_3

JOURNAL FREE ACCESS

Download PDF (238K)
Thermodynamic stability and kinetic folding of α-domain mutants of goat a-lactalbumin

K. Saeki, M. Arai, K. Kuwajima

Article type: Article
2003Volume 43Issue supplement Pages S58-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S58_4

JOURNAL FREE ACCESS

Download PDF (238K)
Trapping of the submillisecond folding intermediates of cytochrome c in a wet porous sol-gel silica

N. Shibayama, S. Saigo

Article type: Article
2003Volume 43Issue supplement Pages S59-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S59_1

JOURNAL FREE ACCESS

Download PDF (264K)
Characterization of hydrophobic cluster in early step of cytochrome c folding

A. Yane, S. takahashi, K. Ishimori, I. Morishima

Article type: Article
2003Volume 43Issue supplement Pages S59-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S59_2

JOURNAL FREE ACCESS

Download PDF (264K)
Folding Mechanism of Single-chain Monellin Based on the Secondary Structure Formation and the Packing of the Hydrophobic Residues

T. Kimura, S. Takahashi, T. Konno, K. Ishimori, I. Morishima

Article type: Article
2003Volume 43Issue supplement Pages S59-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S59_3

JOURNAL FREE ACCESS

Download PDF (264K)
Inhibitor-induced folding of Staphylococcal nuclease

M. Onitsuka, H. Kamikubo, H. Nakagawa, Y. Yamazaki, Y. Imamoto, M. Kat ...

Article type: Article
2003Volume 43Issue supplement Pages S59-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S59_4

JOURNAL FREE ACCESS

Download PDF (264K)
Early Folding Events of Staphylococcal Nuclease Monitored by Single-tryptophan Mutations and ANS Fluorescence

K. Maki, Hong Cheng, Dimitry A. Dolgikh, Heinrich Roder

Article type: Article
2003Volume 43Issue supplement Pages S60-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S60_1

JOURNAL FREE ACCESS

Download PDF (232K)
Main-chain collapse and subsequent tertiary structure formation during apomyoglobin folding

T. Uzawa, T. Kimura, S. Takahashi, K. Ishimori, I. Morishima, S. Akiya ...

Article type: Article
2003Volume 43Issue supplement Pages S60-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S60_2

JOURNAL FREE ACCESS

Download PDF (232K)
Structural analysis of early folding species of dihydrofolate reductase by systematic single amino-acid substitutions

M. Arai, M. Iwakura

Article type: Article
2003Volume 43Issue supplement Pages S60-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S60_3

JOURNAL FREE ACCESS

Download PDF (232K)
Refolding analysls of GFP usmg proline mutant

N. Hirakida, T. Zako, T. Funatsu

Article type: Article
2003Volume 43Issue supplement Pages S60-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S60_4

JOURNAL FREE ACCESS

Download PDF (232K)
NMR study on the unfolding and refolding reactions of pyrrolidone carboxyl peptidase labeled only leucine by ^<15>N from a hyperthermophile.

S. Iimura, H. Yagi, K. Ogasahara, H. Akutsu, Y. Noda, S. Segawa, K. Yu ...

Article type: Article
2003Volume 43Issue supplement Pages S61-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S61_1

JOURNAL FREE ACCESS

Download PDF (254K)
Acid denaturation and refolding of a mutant (Cycle3) of Green Fluorescent Protein

S. Enoki, K. Saeki, K. Kuwajima

Article type: Article
2003Volume 43Issue supplement Pages S61-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S61_2

JOURNAL FREE ACCESS

Download PDF (254K)
Roles of the N-terminal fluctuating domain in folding of coiled coil GCN4-pl'

M. Kinoshita, T. Kimura, S. Takahashi, K. Ishimori, I. Morishima

Article type: Article
2003Volume 43Issue supplement Pages S61-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S61_3

JOURNAL FREE ACCESS

Download PDF (254K)
Restricted contribution of bound peptide residues to the MHC folding

K. Saito, A. Sarai, M. Oda, T. Azuma, H. Kozono

Article type: Article
2003Volume 43Issue supplement Pages S61-
Published: August 25, 2003
Released on J-STAGE: May 01, 2017

DOIhttps://doi.org/10.2142/biophys.43.S61_4

JOURNAL FREE ACCESS

Download PDF (254K)

Register with J-STAGE for free!