Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method. - Yoshifumi Fukunishi; Makoto Suzuki (J. Comput. Chem., 1997)

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. - Anders Wallqvist; Yoshifumi Fukunishi; Lynne Reed Murphy; Addi Fadel; Ronald M. Levy (Bioinform., 2000)

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. - Rie Tatsumi; Yoshifumi Fukunishi; Haruki Nakamura (J. Comput. Chem., 2004)

A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening. - Yoshifumi Fukunishi; Satoru Kubota; Chisato Kanai; Haruki Nakamura (J. Comput. Aided Mol. Des., 2006)

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. - Yoshifumi Fukunishi; Shinichi Hojo; Haruki Nakamura (J. Chem. Inf. Model., 2006)

Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening. - Yoshifumi Fukunishi; Satoru Kubota; Haruki Nakamura (J. Chem. Inf. Model., 2006)

In Silico Drug Screening Based on a Protein-Compound Affinity Matrix. - Yoshifumi Fukunishi (BIOTECHNO, 2008)

Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins. - Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2008)

Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method. - Yoshifumi Fukunishi; Daisuke Mitomo; Haruki Nakamura (J. Chem. Inf. Model., 2009)

In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design. - Yoshifumi Fukunishi; Tadaaki Mashimo; Masaya Orita; Kazuki Ohno; Haruki Nakamura (J. Chem. Inf. Model., 2009)

Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). - Yoshifumi Fukunishi; Kazuki Ohno; Masaya Orita; Haruki Nakamura (J. Chem. Inf. Model., 2010)

Definition of Drug-Likeness for Compound Affinity. - Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2011)

Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes. - Mitsuhito Wada; Eiji Kanamori; Haruki Nakamura; Yoshifumi Fukunishi (J. Chem. Inf. Model., 2011)

Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases. - Yoshifumi Fukunishi; Takashi Kurosawa; Yoshiaki Mikami; Haruki Nakamura (J. Chem. Inf. Model., 2014)

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 (J. Comput. Chem., 2015)

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 (J. Chem. Inf. Model., 2015)

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 (J. Comput. Chem., 2016)

Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. - Junichi Higo; Takeshi Kawabata; Ayumi Kusaka; Kota Kasahara; Narutoshi Kamiya; Ikuo Fukuda; Kentaro Mori; Yutaka Hata; Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2020)

Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. - Junichi Higo; Hajime Takashima; Yoshifumi Fukunishi; Atsushi Yoshimori (J. Comput. Chem., 2021)

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. - Kei Moritsugu; Koh Takeuchi; Narutoshi Kamiya; Junichi Higo; Isao Yasumatsu; Yoshifumi Fukunishi; Ikuo Fukuda (J. Chem. Inf. Model., 2021)