Yoshifumi Fukunishi - My portal

Profile Information

Affiliation: National Institute of Advanced Industrial Science and Technology

Degree: Ph.D(Engineering)

J-GLOBAL ID: 200901030514498002
researchmap Member ID: 5000000719

External link: http://www.aist.go.jp/RESEARCHERDB/cgi-bin/worker_detail.cgi?call=namae&rw_id=Y52155947

Education

Papers

Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications.

Yoshifumi Fukunishi, Yasunobu Yamashita, Tadaaki Mashimo, Haruki Nakamura

Molecular informatics, 37(6-7) e1700120, Jul, 2018 Peer-reviewed
Identification of Mepenzolate Derivatives With Long-Acting Bronchodilatory Activity.

Ken-Ichiro Tanaka, Naoki Yamakawa, Yasunobu Yamashita, Teita Asano, Yuki Kanda, Ayaka Takafuji, Masahiro Kawahara, Mitsuko Takenaga, Yoshifumi Fukunishi, Tohru Mizushima

Frontiers in pharmacology, 9 344-344, 2018 Peer-reviewed
Significance of educational use of drug development program suite myPresto for medical students

Oike M, Kimura C, Fukunishi Y

Journal of Pharmacological Sciences, 133(3) S262, 2017 Peer-reviewed
Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction

Yoshifumi Fukunishi, Satoshi Yamasaki, Isao Yasumatsu, Koh Takeuchi, Takashi Kurosawa, Haruki Nakamura

MOLECULAR INFORMATICS, 36(1-2), Jan, 2017 Peer-reviewed
Variation of Free-Energy Landscape of the p53 C-Terminal Domain Induced by Acetylation: Enhanced Conformational Sampling

Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, Junichi Higo

JOURNAL OF COMPUTATIONAL CHEMISTRY, 37(31) 2687-2700, Dec, 2016 Peer-reviewed
Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics

Yoshifumi Fukunishi, Tadaaki Mashimo, Kiyotaka Misoo, Yoshinori Wakabayashi, Toshiaki Miyaki, Seiji Ohta, Mayu Nakamura, Kazuyoshi Ikeda

CURRENT PHARMACEUTICAL DESIGN, 22(23) 3555-3568, 2016 Peer-reviewed
Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method

Hung Nguyen, Tien Tran, Yoshifumi Fukunishi, Junichi Higo, Haruki Nakamura, Ly Le

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55(9) 1936-1943, Sep, 2015 Peer-reviewed
Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura

JOURNAL OF COMPUTATIONAL CHEMISTRY, 36(20) 1489-1501, Jul, 2015 Peer-reviewed
Structure-Based Development of a Protein-Protein Interaction Inhibitor Targeting Tumor Necrosis Factor Receptor-Associated Factor 6

Jun Moriya, Koh Takeuchi, Kenji Tai, Kenzo Arai, Naoki Kobayashi, Naoki Yoneda, Yoshifumi Fukunishi, Atsushi Inoue, Miho Kihara, Takumi Murakami …

JOURNAL OF MEDICINAL CHEMISTRY, 58(14) 5674-5683, Jul, 2015 Peer-reviewed
Bongkrekic acid as a selective activator of the peroxisome proliferator-activated receptor gamma (PPAR gamma) isoform

Hiroyuki Okazaki, Shuso Takeda, Erika Ikeda, Yoshifumi Fukunishi, Hiroyuki Ishii, Aya Taniguchi, Miki Tokuyasu, Taichi Himeno, Kazuhiro Kakizoe, Kenji Matsumoto …

JOURNAL OF TOXICOLOGICAL SCIENCES, 40(2) 223-233, Apr, 2015 Peer-reviewed
Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases

Yoshifumi Fukunishi, Takashi Kurosawa, Yoshiaki Mikami, Haruki Nakamura

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54(12) 3259-3267, Dec, 2014 Peer-reviewed
Synthesis and biological comparison of enantiomers of mepenzolate bromide, a muscarinic receptor antagonist with bronchodilatory and anti-inflammatory activities

Yasunobu Yamashita, Ken-Ichiro Tanaka, Teita Asano, Naoki Yamakawa, Daisuke Kobayashi, Tomoaki Ishihara, Kengo Hanaya, Mitsuru Shoji, Takeshi Sugai, Mitsuhito Wada …

BIOORGANIC & MEDICINAL CHEMISTRY, 22(13) 3488-3497, Jul, 2014 Peer-reviewed
Structural insights into the function of a thermostable copper-containing nitrite reductase

Yohta Fukuda, Ka Man Tse, Masami Lintuluoto, Yoshifumi Fukunishi, Eiichi Mizohata, Hiroyoshi Matsumura, Hideto Takami, Masaki Nojiri, Tsuyoshi Inoue

JOURNAL OF BIOCHEMISTRY, 155(2) 123-135, Feb, 2014 Peer-reviewed
Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions

Tadaaki Mashimo, Yoshifumi Fukunishi, Narutoshi Kamiya, Yu Takano, Ikuo Fukuda, Haruki Nakamura

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9(12) 5599-5609, Dec, 2013 Peer-reviewed
Molecular modeling of vasopressin receptor and in silico screening of V1b receptor antagonists

Yohsuke Hagiwara, Kazuki Ohno, Masazumi Kamohara, Jun Takasaki, Toshihiro Watanabe, Yoshifumi Fukunishi, Haruki Nakamura, Masaya Orita

Expert Opinion on Drug Discovery, 8(8) 951-964, Aug, 2013 Peer-reviewed
Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules

Yoshifumi Fukunishi, Haruki Nakamura

Pharmaceuticals, 6(5) 604-622, Apr 26, 2013 Peer-reviewed
LigandBox: A database for 3D structures of chemical compounds

Takeshi Kawabata, Yusuke Sugihara, Yoshifumi Fukunishi, Haruki Nakamura

Biophysics (Japan), 9 113-121, 2013 Peer-reviewed
Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking

Yoshifumi Fukunishi, Haruki Nakamura

Pharmaceuticals, 5(12) 1332-1345, Dec 4, 2012 Peer-reviewed
Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation

Yoshifumi Fukunishi, Haruki Nakamura

Pharmaceuticals, 5(10) 1064-1079, Sep 28, 2012 Peer-reviewed
The in silico screening and X-ray structure analysis of the inhibitor complex of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase

Yasuhide Takashima, Eiichi Mizohata, Sudaratana R. Krungkrai, Yoshifumi Fukunishi, Takayoshi Kinoshita, Tsuneaki Sakata, Hiroyoshi Matsumura, Jerapan Krungkrai, Toshihiro Horii, Tsuyoshi Inoue

JOURNAL OF BIOCHEMISTRY, 152(2) 133-138, Aug, 2012 Peer-reviewed

Misc.

Multiple target screening method for robust and accurate in silico ligand screening

Yoshifumi Fukunishi, Yoshiaki Mikami, Satoru Kubota, Haruki Nakamura

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 25(1) 61-70, Sep, 2006
Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes

H Takahashi, M Miyazawa, Y Ina, Y Fukunishi, Y Mizukoshi, H Nakamura, Shimada, I

JOURNAL OF BIOMOLECULAR NMR, 34(3) 167-177, Mar, 2006
Classification of chemical compounds by protein-compound docking for use in designing a focused library

Y Fukunishi, Y Mikami, K Takedomi, M Yamanouchi, H Shima, H Nakamura

JOURNAL OF MEDICINAL CHEMISTRY, 49(2) 523-533, Jan, 2006
Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening

Y Fukunishi, Y Mikami, H Nakamura

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 24(1) 34-45, Sep, 2005
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor

R Tatsumi, Y Fukunishi, H Nakamura

JOURNAL OF COMPUTATIONAL CHEMISTRY, 25(16) 1995-2005, Dec, 2004
Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

YS Watanabe, JG Kim, Y Fukunishi, H Nakamura

CHEMICAL PHYSICS LETTERS, 400(1-3) 258-263, Dec, 2004
Modelling of third cytoplasmic loop of bovine rhodopsin by multicanonical molecular dynamics

YS Watanabe, Y Fukunishi, H Nakamura

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 23(1) 59-68, Sep, 2004
Dynamical origin of enhanced conformational searches of Tsallis statistics sampling

JG Kim, Y Fukunishi, H Nakamura

JOURNAL OF CHEMICAL PHYSICS, 121(3) 1626-1635, Jul, 2004
Average energy guided simulated tempering implemented into molecular dynamics algorithm for protein folding simulation

JG Kim, Y Fukunishi, H Nakamura

CHEMICAL PHYSICS LETTERS, 392(1-3) 34-39, Jul, 2004
Multicanonical molecular dynamics algorithm employing adaptive force-biased iteration scheme

PHYSICAL REVIEW E, 70 057103-, 2004
Stochastic formulation of sampling dynamics in generalized ensemble methods

PHYSICAL REVIEW E, 69(2) 021101-021101, 2004
The filling potential method: A method for estimating the free energy surface for protein-ligand docking

Y Fukunishi, Y Mikami, H Nakamura

JOURNAL OF PHYSICAL CHEMISTRY B, 107(47) 13201-13210, Nov, 2003
dynamical origin of uniform sampling in multicanonical ensemble

PHYSICAL REVIEW E, 67(1) 011105-011105, 2003
Determination of multicanonical weight based on a stochastic model of sampling dynamics

PHYSICAL REVIEW E, 68(2) 021110-021110, 2003

Research Projects

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