Y. Fukunishi

发表

Amino acid translation program for full-length cDNA sequences with frameshift errors.

Y. Hayashizaki, Y. Fukunishi, Yoshihide Hayashizaki, 2001, Physiological genomics.

Classification of chemical compounds by protein-compound docking for use in designing a focused library.

Y. Fukunishi, Haruki Nakamura, Yoshiaki Mikami, 2006, Journal of medicinal chemistry.

Functional annotation of a full-length mouse cDNA collection

C. Bult, S. Batalov, Y. Matsuo, 2001, Nature.

Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.

Y. Fukunishi, V. Dötsch, M. Reese, 2011, Journal of structural biology.

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.

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.

The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein−Ligand Docking

Y. Fukunishi, Haruki Nakamura, Yoshiaki Mikami, 2003 .

Y. Fukunishi, Haruki Nakamura, Yoshiaki Mikami, 2005, Journal of molecular graphics & modelling.

Protein-protein interaction panel using mouse full-length cDNAs.

Y. Hayashizaki, H. Bono, Y. Okazaki, 2001, Genome research.

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.

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.

Mutational Analysis of Block and Facilitation of HERG Current by A Class III Anti-Arrhythmic Agent, Nifekalant

K. Kinoshita, Y. Fukunishi, Haruki Nakamura, 2007, Channels.

Prediction of Positions of Active Compounds Makes It Possible To Increase Activity in Fragment-Based Drug Development

Y. Fukunishi, 2011, Pharmaceuticals.

A2B adenosine receptor inhibition by the dihydropyridine calcium channel blocker nifedipine involves colonic fluid secretion

Y. Fukunishi, T. Mashimo, T. Mizushima, 2020, Scientific Reports.

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.

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.

Structure determination of a protein assembly by amino acid selective cross‐saturation

Y. Fukunishi, Haruki Nakamura, Eiji Kanamori, 2011, Proteins.

Sertraline, chlorprothixene, and chlorpromazine characteristically interact with the REST-binding site of the corepressor mSin3, showing medulloblastoma cell growth inhibitory activities

Y. Fukunishi, H. Nakano, Y. Nishimura, 2018, Scientific Reports.

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

T. Kawabata, Y. Fukunishi, Haruki Nakamura, 2020, bioRxiv.

Prediction of Passive Membrane Permeability by Semi‐Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion

Hironori K. Nakamura, Y. Fukunishi, T. Mashimo, 2019, Molecular informatics.

Y. Fukunishi, Haruki Nakamura, 2014 .

In-silico drug screening method based on the protein-compound affinity matrix using the factor selection technique.

Y. Fukunishi, Haruki Nakamura, S. Murali, 2007, European journal of medicinal chemistry.

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

Y. Fukunishi, Haruki Nakamura, T. Mashimo, 2018, Molecular informatics.

Cannabidiol-2',6'-dimethyl ether as an effective protector of 15-lipoxygenase-mediated low-density lipoprotein oxidation in vitro.

Y. Fukunishi, H. Aramaki, Kazuhito Watanabe, 2011, Biological & pharmaceutical bulletin.

Molecular modeling of vasopressin receptor and in silico screening of V1b receptor antagonists

Y. Fukunishi, Haruki Nakamura, Yohsuke Hagiwara, 2013, Expert opinion on drug discovery.

Calculation of protein-ligand binding free energy using smooth reaction path generation (SRPG) method: a comparison of the explicit water model, gb/sa model and docking score function.

Y. Fukunishi, Haruki Nakamura, J. Higo, 2009, Genome informatics. International Conference on Genome Informatics.

Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Y. Fukunishi, H. Matsuo, M. Lintuluoto, 2012, Biology.

Chemical modification-mediated optimisation of bronchodilatory activity of mepenzolate, a muscarinic receptor antagonist with anti-inflammatory activity.

M. Kawahara, Y. Fukunishi, T. Mizushima, 2019, Bioorganic & medicinal chemistry.

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 .

REPRODUCTION OF THE POTENTIAL OF MEAN FORCE BY A MODIFIED SOLVENT-ACCESSIBLE SURFACE METHOD

Y. Fukunishi, Makoto Suzuki, 1996 .

Protein Interaction Panel Using Mouse Full-Length cDNAs − Protein Material Supplemental

Y. Hayashizaki, H. Bono, Y. Okazaki, 2017 .

Crystallization and preliminary X-ray diffraction analysis of mouse prostaglandin F2α synthase, AKR1B3.

Y. Fukunishi, Y. Urade, E. Mizohata, 2011, Acta crystallographica. Section F, Structural biology and crystallization communications.

Investigation on substrate specificity and catalytic activity of serine protease neuropsin

Y. Fukunishi, J. M. Lintuluoto, M. Lintuluoto, 2022, Biophysics and Physicobiology.

Cluster model study on GaAs epitaxial crystal growth by an arsenic molecular beam III. As4 molecular beam

Y. Fukunishi, H. Nakatsuji, 1994 .

Quantitative Structure‐activity Relationship (QSAR) Models for Docking Score Correction

Y. Fukunishi, Haruki Nakamura, S. Yamasaki, 2016, Molecular informatics.

Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights.

Y. Fukunishi, Haruki Nakamura, A. Kidera, 2004, The Journal of chemical physics.

Coupling of protein surface hydrophobicity change to ATP hydrolysis by myosin motor domain.

Y. Fukunishi, T. Yanagida, Y. Harada, 1997, Biophysical journal.

Structure-Based Development of a Protein-Protein Interaction Inhibitor Targeting Tumor Necrosis Factor Receptor-Associated Factor 6.

Y. Fukunishi, I. Shimada, A. Inoue, 2015, Journal of medicinal chemistry.

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Y. Fukunishi, J. Higo, K. Kasahara, 2022, Biophysical Reviews.

Dynamical origin of enhanced conformational searches of Tsallis statistics sampling.

Y. Fukunishi, Haruki Nakamura, Jae Gil Kim, 2004, The Journal of chemical physics.

Hydrophobic Hydration Analysis on Amino Acid Solutions by the Microwave Dielectric Method

Y. Fukunishi, Makoto Suzuki, T. Kodama, 1997 .

On Ergodicity for Multidimensional Harmonic Oscillator Systems with Nosé – Hoover-type Thermostat

Y. Fukunishi, K. Moritsugu, I. Fukuda, 2021, Regular and Chaotic Dynamics.

Cluster model study on GaAs epitaxial crystal growth by arsenic molecular beam: I. As2 adsorption on a GaAs surface

Y. Fukunishi, H. Nakatsuji, 1993 .

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Y. Fukunishi, J. Higo, K. Kasahara, 2022, Biophysical Reviews.

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

Y. Fukunishi, Makoto Suzuki, 1997 .

Structural insights into the function of a thermostable copper-containing nitrite reductase.

Y. Fukunishi, E. Mizohata, Tsuyoshi Inoue, 2014, Journal of biochemistry.

Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases

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

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..

Modifications for ab initio calculations of the moderately large-embedded-cluster model. Hydrogen adsorption on a lithium surface

Y. Fukunishi, H. Nakatsuji, 1992 .

Catalytic mechanism of the primary human prostaglandin F2α synthase, aldo‐keto reductase 1B1 – prostaglandin D2 synthase activity in the absence of NADP(H)

Y. Fukunishi, Y. Urade, Tsuyoshi Inoue, 2011, The FEBS journal.

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation

Y. Fukunishi, K. Moritsugu, J. Higo, 2021, J. Chem. Inf. Model..

Synthesis and biological comparison of enantiomers of mepenzolate bromide, a muscarinic receptor antagonist with bronchodilatory and anti-inflammatory activities.

Y. Fukunishi, Kengo Hanaya, T. Mashimo, 2014, Bioorganic & medicinal chemistry.

Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities

T. Kawabata, Y. Fukunishi, Haruki Nakamura, 2021, Scientific Reports.

Instructions for use Title Protein-Protein Interaction Panel Using Mouse

Y. Hayashizaki, H. Bono, Y. Okazaki, 2017 .

Identification of a novel member of the snail/Gfi-1 repressor family, mlt 1, which is methylated and silenced in liver tumors of SV40 T antigen transgenic mice.

J. Kawai, Y. Hayashizaki, Y. Okazaki, 2001, Cancer research.

Tumors of SV 40 T Antigen Transgenic Mice Which Is Methylated and Silenced in Liver mlt 1 , Family , Repressor Snail / Gfi-1 Identification of a Novel Member of the Updated Version

J. Kawai, Y. Hayashizaki, Y. Okazaki, 2001 .

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..

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..

Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library.

Piero Carninci, Y. Hayashizaki, Y. Fukunishi, 2001, Genome research.

A novel microbial infection-responsive drug release system.

Y. Fukunishi, Y. Suzuki, M. Tanihara, 1999, Journal of pharmaceutical sciences.

Sertraline, chlorprothixene, and chlorpromazine characteristically interact with the REST-binding site of the corepressor mSin3, showing medulloblastoma cell growth inhibitory activities

Y. Fukunishi, H. Nakano, Y. Nishimura, 2018, Scientific Reports.

Bongkrekic acid as a selective activator of the peroxisome proliferator-activated receptor γ (PPARγ) isoform.

Y. Fukunishi, H. Aramaki, M. Shindo, 2015, The Journal of toxicological sciences.

The Trial of Drug Discovery using the In-Silico Screening Methods Developed by Pharmaceutical Innovation Value Chain

Y. Fukunishi, Haruki Nakamura, Y. Okuno, 2010 .

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..

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.

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 .

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Y. Fukunishi, H. Kono, J. Higo, 2022, Scientific Reports.

Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water

Y. Fukunishi, Shinji Iida, 2021, BBA Advances.

An accurate pharmacophore mapping method by NMR spectroscopy.

Y. Fukunishi, I. Shimada, Hideo Takahashi, 2012, Angewandte Chemie.

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

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

Theoretical study of the hydrogen chemisorption on a ZnO surface

Y. Fukunishi, H. Nakatsuji, 1992 .

Dipped adcluster model for chemisorptions and catalytic reactions on a metal surface: Image force correction and applications to Pd-O2 adclusters

Y. Fukunishi, H. Nakatsuji, H. Nakai, 1991 .

Structural ensemble in computational drug screening

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

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.

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..

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.

Utilization of Methyl Proton Resonances in Cross-Saturation Measurement for Determining the Interfaces of Large Protein–Protein Complexes

Y. Fukunishi, Haruki Nakamura, I. Shimada, 2006, Journal of biomolecular NMR.

Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations

Y. Fukunishi, H. Nakai, Junichi Ono, 2022, Chemical Physics Letters.

Molecular Dynamics Simulation Study on Allosteric Regulation of CD44-Hyaluronan Binding as a Force Sensing Mechanism

Y. Fukunishi, J. M. Lintuluoto, M. Lintuluoto, 2021, ACS omega.

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

Y. Fukunishi, J. Higo, N. Kamiya, 2021, Scientific Reports.

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.

Generalized–ensemble method study: A helix‐mimetic compound inhibits protein–protein interaction by long‐range and short‐range intermolecular interactions

Y. Fukunishi, J. Higo, A. Yoshimori, 2021, J. Comput. Chem..

Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-Based Drug Design.

Hironori K. Nakamura, Y. Fukunishi, T. Mashimo, 2020, The journal of physical chemistry. B.

Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

Y. Fukunishi, Haruki Nakamura, Yukihisa S. Watanabe, 2004 .

Finding ligands for G protein-coupled receptors based on the protein-compound affinity matrix.

Y. Fukunishi, Haruki Nakamura, Satoru Kubota, 2007, Journal of Molecular Graphics and Modelling.

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..

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.

Definition of Drug-Likeness for Compound Affinity

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

Identification of Mepenzolate Derivatives With Long-Acting Bronchodilatory Activity

M. Kawahara, Y. Fukunishi, T. Mizushima, 2018, Front. Pharmacol..

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.

Determination of multicanonical weight based on a stochastic model of sampling dynamics.

Y. Fukunishi, Haruki Nakamura, A. Kidera, 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding

Y. Fukunishi, Haruki Nakamura, Yukihisa S. Watanabe, 2006, Biophysics.

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

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

On Ergodicity for Multidimensional Harmonic Oscillator Systems with Nosé – Hoover-type Thermostat

Y. Fukunishi, K. Moritsugu, I. Fukuda, 2020, 2008.07917.

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

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

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..

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

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

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..

Prediction of human cDNA from its homologous mouse full‐length cDNA and human shotgun database

Y. Hayashizaki, Harukazu Suzuki, Y. Fukunishi, 1999, FEBS letters.

sequences with frameshift errors Amino acid translation program for full-length cDNA

Y. Hayashizaki, K. Shinozaki, M. Blaxter, 2015 .

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

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

Folding‐unfolding energy change of a simple sphere model protein and an energy landscape of the folding process

Y. Fukunishi, 1998, Proteins.

β‐Turn structure and intramolecular interaction of tetrapeptides containing Asp and Lys

Y. Fukunishi, Y. Inoue, H. Ishii, 1985 .

Cluster model study on GaAs epitaxial crystal growth by arsenic molecular beam : II. Mechanism involving a GaAs2 intermediate cluster

Y. Fukunishi, H. Nakatsuji, 1993 .

Synthesis and biological comparison of enantiomers of mepenzolate bromide, a muscarinic receptor antagonist with bronchodilatory and anti-inflammatory activities.

Y. Fukunishi, Kengo Hanaya, T. Mashimo, 2014, Bioorganic & medicinal chemistry.

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.

Development of Chemical Compound Libraries for In Silico Drug Screening.

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