List of works - Yoshifumi Fukunishi

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

scientific article

A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening

scientific article published on 01 April 2006

An accurate pharmacophore mapping method by NMR spectroscopy

scientific article published on 30 December 2011

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

scientific article

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

scientific article published on January 2015

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

scientific article

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

scientific article published on 10 March 2011

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

scientific article published in January 2006

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

scientific article

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

scientific article

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

scientific article

Definition of Drug-Likeness for Compound Affinity ⬇️

scientific article published on April 27, 2011

Development of Chemical Compound Libraries for In Silico Drug Screening

scientific article

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

scientific article published on 10 May 2006

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

scientific article

Functional annotation of a full-length mouse cDNA collection

scientific article (publication date: 8 February 2001)

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

scientific article published on 01 September 2004

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

scientific article published on 31 January 2006

Identification of Mepenzolate Derivatives With Long-Acting Bronchodilatory Activity.

scientific article

Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules

scientific article published on 26 April 2013

In silico fragment screening by replica generation (FSRG) method for fragment-based drug design

scientific article

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

scientific article published on 13 January 2007

LigandBox: A database for 3D structures of chemical compounds.

scientific article published on 7 August 2013

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

scientific article

Modelling of third cytoplasmic loop of bovine rhodopsin by multicanonical molecular dynamics

scientific article published on 01 September 2004

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

scientific article published on 19 November 2013

Molecular modeling of vasopressin receptor andin silicoscreening of V1b receptor antagonists ⬇️

scientific article published on May 17, 2013

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

scientific article published on 22 December 2005

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

scientific article

Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening.

scientific article

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

scientific article published on 14 October 2019

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

scientific article published in December 1999

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

scientific article published on January 1, 2011

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

scientific article published on 12 July 2007

Protein-ligand binding free energy calculation by the Smooth Reaction Path Generation (SRPG) Method

scientific article published in August 2009

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

scientific article published on 3 September 2011

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

scientific article published on 29 April 2016

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

scientific article published on 9 April 2011

Selection of in silico drug screening results for G-protein-coupled receptors by using universal active probes

scientific article published on 29 August 2011

Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening

scientific article published on 01 September 2005

Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation

scientific article published on 28 September 2012

Stochastic formulation of sampling dynamics in generalized ensemble methods

scientific article published on 10 February 2004

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

scientific article

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

scientific article published on 14 July 2015

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

scientific article published on May 2009

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

scientific article published on 30 April 2014

The in silico screening and X-ray structure analysis of the inhibitor complex of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase

scientific article

Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes

scientific article published on 01 March 2006

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

scientific article published on 13 October 2016

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

scientific article published on 4 June 2015

List of works by Yoshifumi Fukunishi

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

A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening

An accurate pharmacophore mapping method by NMR spectroscopy

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

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

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

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

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

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

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

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

Definition of Drug-Likeness for Compound Affinity ⬇️

Development of Chemical Compound Libraries for In Silico Drug Screening

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

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

Functional annotation of a full-length mouse cDNA collection

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

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

Identification of Mepenzolate Derivatives With Long-Acting Bronchodilatory Activity.

Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules

In silico fragment screening by replica generation (FSRG) method for fragment-based drug design

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

LigandBox: A database for 3D structures of chemical compounds.

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

Modelling of third cytoplasmic loop of bovine rhodopsin by multicanonical molecular dynamics

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

Molecular modeling of vasopressin receptor andin silicoscreening of V1b receptor antagonists ⬇️

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

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

Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening.

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

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

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

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

Protein-ligand binding free energy calculation by the Smooth Reaction Path Generation (SRPG) Method

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

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

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

Selection of in silico drug screening results for G-protein-coupled receptors by using universal active probes

Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening

Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation

Stochastic formulation of sampling dynamics in generalized ensemble methods

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

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

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

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

The in silico screening and X-ray structure analysis of the inhibitor complex of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase

Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes

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

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