Takao Yoda - My portal

Profile Information

Affiliation: Lecturer, Nagahama Institute of Bio-Science and Technology

Degree: 博士（理学）

J-GLOBAL ID: 200901099093675287
researchmap Member ID: 5000063916

Research Interests

Research Areas

Life sciences / Biophysics /

Research History

Education

- 2000

The University of Tokyo

Papers

Exonuclease processivity of archaeal replicative DNA polymerase in association with PCNA is expedited by mismatches in DNA

Takuya Yoda, Maiko Tanabe, Toshiyuki Tsuji, Takao Yoda, Sonoko Ishino, Tsuyoshi Shirai, Yoshizumi Ishino, Haruko Takeyama, Hirokazu Nishida

SCIENTIFIC REPORTS, 7 44582, Mar, 2017 Peer-reviewed
Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling

Toshiyuki Tsuji, Takao Yoda, Tsuyoshi Shirai

SCIENTIFIC REPORTS, 5 16341, Nov, 2015 Peer-reviewed
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, Yuji Sugita

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 5(4) 310-323, Jul, 2015 Peer-reviewed
Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations

Takao Yoda, Yuji Sugita, Yuko Okamoto

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82(6) 933-943, Jun, 2014 Peer-reviewed
Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations

Takao Yoda, Yuji Sugita, Yuko Okamoto

BIOPHYSICAL JOURNAL, 99(5) 1637-1644, Sep, 2010 Peer-reviewed
Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

Y. Kawashima, Y. C. Sasaki, Y. Sugita, T. Yoda, Y. Okamoto

MOLECULAR SIMULATION, 33(1-2) 97-102, Jan, 2007
Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: A molecular dynamics study

Yuji Sugita, Naoyuki Miyashita, Takao Yoda, Mitsunori Ikeguchi, Chikashi Toyoshima

BIOCHEMISTRY, 45(39) 11752-11761, Oct, 2006
Effects of the fixed end in single-molecule imaging techniques: A replica-exchange molecular dynamics simulation study

Y Kawashima, Y Sugita, T Yoda, Y Okamoto

CHEMICAL PHYSICS LETTERS, 414(4-6) 449-455, Oct, 2005 Peer-reviewed
Structures of a peptide fragment Of beta(2)-microglobulin studied by replica-exchange molecular dynamics simulations - Towards the understanding of the mechanism of amyloid formation

M Nishino, Y Sugita, T Yoda, Y Okamoto

FEBS LETTERS, 579(24) 5425-5429, Oct, 2005 Peer-reviewed
Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations

T Yoda, Y Sugita, Y Okamoto

CHEMICAL PHYSICS, 307(2-3) 269-283, Dec, 2004 Peer-reviewed
Localized nature of the transition-state structure in goat alpha-lactalbumin folding

K Saeki, M Arai, T Yoda, M Nakao, K Kuwajima

JOURNAL OF MOLECULAR BIOLOGY, 341(2) 589-604, Aug, 2004 Peer-reviewed
Comparisons of force fields for proteins by generalized-ensemble simulations

T Yoda, Y Sugita, Y Okamoto

CHEMICAL PHYSICS LETTERS, 386(4-6) 460-467, Mar, 2004 Peer-reviewed
K.Horii, M.Saito, T.Yoda, K.Tsumoto, M.Matsushima, K.Kuwajima and I.Kumagai,

Proteins, 45, 16-29, 2001
Folding-unfolding of goat alpha-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations

T Yoda, M Saito, M Arai, K Horii, K Tsumoto, M Matsushima, Kumagai, I, K Kuwajima

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 42(1) 49-65, Jan, 2001 Peer-reviewed
Effect of the extra N-terminal methionine residue on the stability and folding of recombinant alpha-lactalbumin expressed in Escherichia coli

TK Chaudhuri, K Horii, T Yoda, M Arai, S Nagata, TP Terada, H Uchiyama, T Ikura, K Tsumoto, H Kataoka, M Matsushima, K Kuwajima, Kumagai, I

JOURNAL OF MOLECULAR BIOLOGY, 285(3) 1179-1194, Jan, 1999 Peer-reviewed

Misc.

Folding Simulation of a Mini Protein with a Hydrophobic Core and α-helices

YODA Takao, SUGITA Yuji, OKAMOTO Yuko

Seibutsu Butsuri, 52(1) 22-23, Jan 25, 2012
Force Field Functions for Molecular Simulations of Protein Systems(Current Topics)

Sakae Yoshitake, Yoda Takao, Sugita Yuji, Okamoto Yuko

Butsuri, 67(5) 343-349, 2012
マルチカノニカルレプリカ交換分子動力学法による小蛋白質の折れ畳みシミュレーション (特集拡張アンサンブル法)

依田隆夫, 杉田有治, 岡本祐幸

アンサンブル, 12(2) 15-18, Apr, 2010
タンパク質系のポテンシャル関数の比較と改良

榮慶丈, 依田隆夫, 杉田有冶, 岡本祐幸

アンサンブル, 11(3) 3_8-3_12, 2009
Kinetic folding reactions and molecular dynamics simulations of alpha-lactalbumin

Takao Yoda, Minoru Saito, Munehito Arai, Katsunori Horii, Kouhei Tsumoto, Masaaki Matsushima, Izumi Kumagai, Tapan K. Chaudhuri, Kunihiro Kuwajima

In “Old and New Views of Protein Folding” (Kuwajima & Arai eds), 155-162, 1999

Professional Memberships

Research Projects

Protein folding studies by computer simulations