Yoshifumi Fukunishi

Publication Activity (10 Years)

Years Active: 1997-2021
Publications (10 Years): 4

Top Topics

Protein Interaction

Energy Landscape

Tandem Mass Spectra

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Kei Moritsugu, Koh Takeuchi, Narutoshi Kamiya, Junichi Higo, Isao Yasumatsu, Yoshifumi Fukunishi, Ikuo Fukuda
Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. J. Chem. Inf. Model. 61 (4) (2021)
Junichi Higo, Hajime Takashima, Yoshifumi Fukunishi, Atsushi Yoshimori
Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. J. Comput. Chem. 42 (14) (2021)
Junichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. J. Chem. Inf. Model. 60 (10) (2020)
Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, Junichi Higo
Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling. J. Comput. Chem. 37 (31) (2016)
Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura
Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. J. Comput. Chem. 36 (20) (2015)
Hung Nguyen, Tien Tran, Yoshifumi Fukunishi, Junichi Higo, Haruki Nakamura, Ly Le
Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. 55 (9) (2015)
Yoshifumi Fukunishi, Takashi Kurosawa, Yoshiaki Mikami, Haruki Nakamura
Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases. J. Chem. Inf. Model. 54 (12) (2014)
Mitsuhito Wada, Eiji Kanamori, Haruki Nakamura, Yoshifumi Fukunishi
Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes. J. Chem. Inf. Model. 51 (9) (2011)
Yoshifumi Fukunishi, Haruki Nakamura
Definition of Drug-Likeness for Compound Affinity. J. Chem. Inf. Model. 51 (5) (2011)
Yoshifumi Fukunishi, Kazuki Ohno, Masaya Orita, Haruki Nakamura
Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). J. Chem. Inf. Model. 50 (7) (2010)
Yoshifumi Fukunishi, Tadaaki Mashimo, Masaya Orita, Kazuki Ohno, Haruki Nakamura
In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design. J. Chem. Inf. Model. 49 (4) (2009)
Yoshifumi Fukunishi, Daisuke Mitomo, Haruki Nakamura
Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. 49 (8) (2009)
Yoshifumi Fukunishi
In Silico Drug Screening Based on a Protein-Compound Affinity Matrix. BIOTECHNO (2008)
Yoshifumi Fukunishi, Haruki Nakamura
Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins. J. Chem. Inf. Model. 48 (1) (2008)
Yoshifumi Fukunishi, Shinichi Hojo, Haruki Nakamura
An Efficient in Silico Screening Method Based on the Protein-Compound Affinity Matrix and Its Application to the Design of a Focused Library for Cytochrome P450 (CYP) Ligands. J. Chem. Inf. Model. 46 (6) (2006)
Yoshifumi Fukunishi, Satoru Kubota, Haruki Nakamura
Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening. J. Chem. Inf. Model. 46 (5) (2006)
Yoshifumi Fukunishi, Satoru Kubota, Chisato Kanai, Haruki Nakamura
A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening. J. Comput. Aided Mol. Des. 20 (4) (2006)
Rie Tatsumi, Yoshifumi Fukunishi, Haruki Nakamura
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. J. Comput. Chem. 25 (16) (2004)
Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinform. 16 (11) (2000)
Yoshifumi Fukunishi, Makoto Suzuki
Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method. J. Comput. Chem. 18 (13) (1997)