Yoshifumi Fukunishi

发表

LigandBox: A database for 3D structures of chemical compounds

Takeshi Kawabata, Haruki Nakamura, Yusuke Sugihara, 2013, Biophysics.

Structural ensemble in computational drug screening

Yoshifumi Fukunishi, Y. Fukunishi, 2010, Expert opinion on drug metabolism & toxicology.

In Silico Drug Screening Based on a Protein-Compound Affinity Matrix

Yoshifumi Fukunishi, 2008, 2008 International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies.

Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method

Makoto Suzuki, Yoshifumi Fukunishi, 1997, J. Comput. Chem..

Virtual‐system‐coupled adaptive umbrella sampling to compute free‐energy landscape for flexible molecular docking

Haruki Nakamura, Kota Kasahara, Bhaskar Dasgupta, 2015, J. Comput. Chem..

Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics

Yoshifumi Fukunishi, Tadaaki Mashimo, Mayu Nakamura, 2016, Current pharmaceutical design.

Development of Chemical Compound Libraries for In Silico Drug Screening.

Yoshifumi Fukunishi, Masami Lintuluoto, Y. Fukunishi, 2010, Current computer-aided drug design.

A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening

Haruki Nakamura, Satoru Kubota, Yoshifumi Fukunishi, 2008, Advances and applications in bioinformatics and chemistry : AABC.

Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling.

Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya, 2020, Journal of chemical information and modeling.

Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening

Haruki Nakamura, Satoru Kubota, Yoshifumi Fukunishi, 2006, J. Chem. Inf. Model..

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

Haruki Nakamura, Yoshifumi Fukunishi, Shinichi Hojo, 2006, J. Chem. Inf. Model..

A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening

Haruki Nakamura, Satoru Kubota, Yoshifumi Fukunishi, 2006, J. Comput. Aided Mol. Des..

Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method

Haruki Nakamura, Ly Le, Hung Nguyen, 2015, J. Chem. Inf. Model..

:- Development of 3D-compound database -

Haruki Nakamura, Yoshifumi Fukunishi, Kohta Sakai, 2009 .

Definition of Drug-Likeness for Compound Affinity

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2011, J. Chem. Inf. Model..

Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method

Haruki Nakamura, Yoshifumi Fukunishi, Daisuke Mitomo, 2009, J. Chem. Inf. Model..

[New progress in crystallization technology of membrane protein and introduction of pharamaceutical innovation value chain].

Haruki Nakamura, Isao Nakanishi, Tsuyoshi Inoue, 2008, Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan.

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases

Ronald M. Levy, Anders Wallqvist, Yoshifumi Fukunishi, 2000, Bioinform..

Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs)

Haruki Nakamura, Yoshifumi Fukunishi, Kazuki Ohno, 2010, J. Chem. Inf. Model..

Post processing of protein-compound docking for fragment-based drug discovery (FBDD): in-silico structure-based drug screening and ligand-binding pose prediction.

Yoshifumi Fukunishi, Y. Fukunishi, 2010, Current topics in medicinal chemistry.

Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins

Haruki Nakamura, Yoshifumi Fukunishi, 2008, J. Chem. Inf. Model..

Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

Haruki Nakamura, Yoshifumi Fukunishi, Junichi Higo, 2016, J. Comput. Chem..

Structure-based drug screening and ligand-based drug screening with machine learning.

Yoshifumi Fukunishi, Y. Fukunishi, 2009, Combinatorial chemistry & high throughput screening.

Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes

Haruki Nakamura, Mitsuhito Wada, Yoshifumi Fukunishi, 2011, J. Chem. Inf. Model..

Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases

Haruki Nakamura, Yoshifumi Fukunishi, Takashi Kurosawa, 2014, J. Chem. Inf. Model..

In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design

Haruki Nakamura, Yoshifumi Fukunishi, Kazuki Ohno, 2009, J. Chem. Inf. Model..

Average energy guided simulated tempering implemented into molecular dynamics algorithm for protein folding simulation

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2004 .

Integration of Ligand-Based Drug Screening with Structure-Based Drug Screening by Combining Maximum Volume Overlapping Score with Ligand Doscking

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2012, Pharmaceuticals.

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

Haruki Nakamura, Yoshifumi Fukunishi, Yoshiaki Mikami, 2006, Journal of molecular graphics & modelling.

Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening.

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2006 .

Dynamical origin of uniform sampling in multicanonical ensemble.

Haruki Nakamura, Yoshifumi Fukunishi, Jae Gil Kim, 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

Protein-ligand docking guided by ligand pharmacophore-mapping experiment by NMR.

Haruki Nakamura, Koh Takeuchi, Hideo Takahashi, 2011, Journal of molecular graphics & modelling.

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2004, J. Comput. Chem..

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2009, Journal of biomedicine & biotechnology.

Quantitative analysis of aggregation-solubility relationship by in-silico solubility prediction

Haruki Nakamura, Yoshifumi Fukunishi, Masaya Orita, 2010 .

In silico prediction of the chemical block of human ether-a-go-go-related gene (hERG) K+ current.

Haruki Nakamura, Yoshifumi Fukunishi, Narutoshi Kamiya, 2008, The journal of physiological sciences : JPS.

In silico prediction of the chemical block of human ether-a-go-go-related gene (hERG) K+ current.

Haruki Nakamura, Yoshifumi Fukunishi, Narutoshi Kamiya, 2008, The journal of physiological sciences : JPS.

Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions.

Haruki Nakamura, Yoshifumi Fukunishi, Narutoshi Kamiya, 2013, Journal of chemical theory and computation.

Prediction of protein-ligand complex structure by docking software guided by other complex structures.

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2008, Journal of molecular graphics & modelling.

Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

Haruki Nakamura, Mitsuhito Wada, Yoshifumi Fukunishi, 2019, Protein engineering, design & selection : PEDS.

Improved Estimation of Protein-Ligand Binding Free Energy by Using the Ligand-Entropy and Mobility of Water Molecules

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2013, Pharmaceuticals.

GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics.

Kentaro Mori, Yoshifumi Fukunishi, Junichi Higo, 2020, Biophysics and physicobiology.

Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2012, Pharmaceuticals.

Prediction of ligand‐binding sites of proteins by molecular docking calculation for a random ligand library

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2011, Protein science : a publication of the Protein Society.

A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method.

Haruki Nakamura, Yoshifumi Fukunishi, Y. Fukunishi, 2009, Journal of molecular graphics & modelling.