H. Kokubo

发表

Design and synthesis of potent and selective pyridazin-4(1H)-one-based PDE10A inhibitors interacting with Tyr683 in the PDE10A selectivity pocket.

M. Yoshikawa, T. Hitaka, Tomoaki Hasui, 2016, Bioorganic & medicinal chemistry.

Ab Initio prediction of protein–ligand binding structures by replica‐exchange umbrella sampling simulations

Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo, 2011, J. Comput. Chem..

Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation

Y. Okamoto, H. Kokubo, 2004 .

Prediction of membrane protein structures by replica-exchange Monte Carlo simulations: case of two helices.

Y. Okamoto, H. Kokubo, 2004, The Journal of chemical physics.

Solvation free energies of alanine peptides: the effect of flexibility.

Robert C. Harris, H. Kokubo, D. Asthagiri, 2013, The journal of physical chemistry. B.

Backbone additivity in the transfer model of protein solvation

Gillian C. Lynch, H. Kokubo, B. Pettitt, 2010, Protein science : a publication of the Protein Society.

Peptide conformational preferences in osmolyte solutions: transfer free energies of decaalanine.

H. Kokubo, B. Pettitt, Char Y Hu, 2011, Journal of the American Chemical Society.

Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion.

A. Kidera, H. Kokubo, Toshimasa Tanaka, 2018, The Journal of chemical physics.

Molecular basis of the apparent near ideality of urea solutions.

B Montgomery Pettitt, Hironori Kokubo, H. Kokubo, 2007, Biophysical journal.

Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study

H. Kokubo, Kai Liu, 2017, J. Chem. Inf. Model..

Predictions of tertiary stuctures of $\alpha$-helical membrane proteins by replica-exchange method with consideration of helix deformations

Y. Okamoto, H. Kokubo, Ryo Urano, 2014, 1409.5788.

Trimethylamine N‐oxide influence on the backbone of proteins: An oligoglycine model

B Montgomery Pettitt, Hironori Kokubo, Gillian C. Lynch, 2009, Proteins.

Discovery of Clinical Candidate N-((1S)-1-(3-Fluoro-4-(trifluoromethoxy)phenyl)-2-methoxyethyl)-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915): A Highly Potent, Selective, and Brain-Penetrating Phosphodiesterase 2A Inhibitor for the Treatment of Cognitive Disorders.

H. Kokubo, H. Oki, T. Taniguchi, 2017, Journal of medicinal chemistry.

Discovery of 1-[2-fluoro-4-(1H-pyrazol-1-yl)phenyl]-5-methoxy-3-(1-phenyl-1H-pyrazol-5-yl)pyridazin-4(1H)-one (TAK-063), a highly potent, selective, and orally active phosphodiesterase 10A (PDE10A) inhibitor.

Hironori Kokubo, Makoto Fushimi, Kosuke Nakashima, 2014, Journal of medicinal chemistry.

Classification and Prediction of Low-Energy Membrane Protein Helix Configurations by Replica-Exchange Monte Carlo Method

Y. Okamoto, H. Kokubo, 2004 .

Prediction of transmembrane helix configurations by replica-exchange simulations

Yuko Okamoto, Hironori Kokubo, Y. Okamoto, 2003, cond-mat/0309338.

Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors.

S. Aparicio, G. Morin, H. Kokubo, 2018, Journal of medicinal chemistry.

Design and synthesis of a novel 2-oxindole scaffold as a highly potent and brain-penetrant phosphodiesterase 10A inhibitor.

M. Yoshikawa, J. Kunitomo, H. Kokubo, 2015, Bioorganic & medicinal chemistry.

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo, 2013, J. Comput. Chem..

Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations

Kai Liu, Hironori Kokubo, Etsurou Watanabe, 2017, Journal of Computer-Aided Molecular Design.

Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations

Hironori Kokubo, Kai Liu, H. Kokubo, 2020, Journal of Computer-Aided Molecular Design.

Prediction of Protein-Ligand Binding Structures by Replica-Exchange Umbrella Sampling Simulations: Application to Kinase Systems.

Toshimasa Tanaka, Hironori Kokubo, Yuko Okamoto, 2013, Journal of chemical theory and computation.

Dependency of ligand free energy landscapes on charge parameters and solvent models

Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo, 2010, J. Comput. Aided Mol. Des..

Ligand docking simulations by generalized-ensemble algorithms.

Yuko Okamoto, Hironori Kokubo, Y. Okamoto, 2013, Advances in protein chemistry and structural biology.

Uncovering abnormal changes in logP after fluorination using molecular dynamics simulations

Kai Liu, Hironori Kokubo, H. Kokubo, 2019, Journal of Computer-Aided Molecular Design.

Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density using proximal Radial Distribution Functions.

B Montgomery Pettitt, Hironori Kokubo, H. Kokubo, 2011, The journal of physical chemistry letters.

Preferential solvation in urea solutions at different concentrations: properties from simulation studies.

B Montgomery Pettitt, Hironori Kokubo, H. Kokubo, 2007, The journal of physical chemistry. B.

Prediction of Ligand Binding Affinity by the Combination of Replica-Exchange Method and Double-Decoupling Method.

Yuko Okamoto, Hironori Kokubo, Y. Okamoto, 2014, Journal of chemical theory and computation.

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

Y. Okamoto, H. Kokubo, Toshimasa Tanaka, 2013, J. Comput. Chem..

Ab Initio prediction of protein–ligand binding structures by replica‐exchange umbrella sampling simulations

Y. Okamoto, H. Kokubo, Toshimasa Tanaka, 2011, J. Comput. Chem..

Dependency of ligand free energy landscapes on charge parameters and solvent models

Y. Okamoto, H. Kokubo, Toshimasa Tanaka, 2010, J. Comput. Aided Mol. Des..

Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations.

Y. Okamoto, H. Kokubo, 2009, Biophysical journal.

Replica-exchange methods and predictions of helix configurations of membrane proteins

Yuko Okamoto, Hironori Kokubo, Y. Okamoto, 2006 .