S. Sakuraba

发表

Detecting coupled collective motions in protein by independent subspace analysis.

Y. Joti, A. Kitao, S. Sakuraba, 2010, The Journal of chemical physics.

Critical Roles for Coiled-Coil Dimers of Butyrophilin 3A1 in the Sensing of Prenyl Pyrophosphates by Human Vγ2Vδ2 T Cells

Yoshimasa Tanaka, S. Sakuraba, Hong Wang, 2019, The Journal of Immunology.

A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin

H. Yoshida, B. Mikami, A. Itoh, 2020, Nature Communications.

A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method.

A. Kitao, N. Matubayasi, S. Sakuraba, 2013, Physical chemistry chemical physics : PCCP.

Discovery of imidazo[1,2-a]pyridines as potent MCH1R antagonists.

H. Iwaasa, S. Sakuraba, A. Kanatani, 2009, Bioorganic & medicinal chemistry letters.

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

K. Asai, T. Kameda, S. Sakuraba, 2015, The journal of physical chemistry letters.

Practical Asymmetric Synthesis of (R)-Fluoxetine Hydrochloride Catalyzed by (2S, 4S)-4-Dicyclohexylphosphino-2-diphenylphosphinomethyl-1-(N-methylcarbamoyl)pyrrolidine-Rhodium Complex1

S. Sakuraba, K. Achiwa, 1991 .

An efficient synthesis of optically active eprozinol

S. Sakuraba, K. Achiwa, N. Nakajima, 1993 .

Efficient Asymmetric Hydrogenation of β- and γ-Amino Ketone Derivatives Leading to Practical Synthesis of Fluoxetine and Eprozinol

S. Sakuraba, K. Achiwa, 1995 .

Efficient Asymmetric Hydrogenation of γ-Amino Ketone Hydrochloride Derivatives Catalyzed by (2S,4S)-4-Dicyclohexylphosphino-2-diphenylphosphinomethyl-1-(N-methylcarbamoyl)-pyrrolidine(MCCPM)-Rhodium complex1

S. Sakuraba, K. Achiwa, N. Nakajima, 2002 .

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation.

I. Fukuda, S. Sakuraba, K. Kasahara, 2018, The journal of physical chemistry. B.

Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach

J. Iwakiri, K. Asai, Michiaki Hamada, 2018, bioRxiv.

Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

O. Nureki, H. Kono, T. Nishizawa, 2021, Nature Communications.

Prediction of Ciclesonide Binding Site on Middle-East Respiratory Syndrome Coronavirus Nsp15 Multimer by Molecular Dynamics Simulations

H. Kono, S. Sakuraba, 2021 .

Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules

H. Kono, Jinzen Ikebe, S. Sakuraba, 2014, J. Comput. Chem..

The binding affinity of uncharged aromatic solutes for negatively charged resins is enhanced by cations via cation-π interactions: The case of sodium ion and arginine.

T. Arakawa, T. Kameda, K. Shiraki, 2019, Journal of chromatography. A.

Salt-dependent elution of uncharged aromatic solutes in ion-exchange chromatography.

T. Arakawa, T. Kameda, K. Shiraki, 2018, Journal of chromatography. A.

Structure--activity relationships of 1beta-methyl-2-(5-phenylpyrrolidin-3-ylthio)carbapenems.

Hiroki Sato, S. Sakuraba, H. Morishima, 2002, Bioorganic & Medicinal Chemistry.

Practical synthesis of a 1beta-methylcarbapenem, J-111,225, using 4-mercapto-2-[4-(N-methylaminomethyl)phenyl]pyrrolidine as a precursor.

S. Sakuraba, H. Satō, H. Morishima, 2001, Chemical & pharmaceutical bulletin.

Short synthesis of (+)-cylindricine C by using a catalytic asymmetric Michael reaction with a two-center organocatalyst.

S. Sakuraba, M. Shibasaki, T. Ohshima, 2006, Angewandte Chemie.

Asymmetric Heck-type Hydroarylation of Norbornene with Phenyl Triflate Catalyzed by Palladium Complexes of Chiral (β-N-Sulfonylaminoalkyl)phosphines1

S. Sakuraba, K. Achiwa, K. Awano, 1994 .

Correlation of X-ray crystal structures of chiral bisphosphine-rhodium catalysts and the absolute configuration of the products resulted by their asymmetric hydrogenations☆

S. Sakuraba, K. Achiwa, T. Morimoto, 1991 .

Asymmetric reactions catalyzed by chiral metal complexes. 41. Highly efficient asymmetric hydrogenation of amino ketone derivatives leading to practical syntheses of (S)-propranolol and related compounds

S. Sakuraba, K. Achiwa, H. Takeda, 1990 .

Practical Synthesis of a 1β‐Methylcarbapenem, J‐111,225, Using 4‐Mercapto‐2‐[4‐(N‐methylaminomethyl)phenyl]pyrrolidine as a Precursor.

S. Sakuraba, H. Morishima, Koji Yamada, 2001 .

Discovery of novel trans-3,5-disubstituted pyrrolidinylthio-1beta-methylcarbapenems.

Y. Tsuchiya, S. Sakuraba, H. Satō, 2000, Bioorganic & medicinal chemistry.

A novel 1beta-methylcarbapenem, J-111,225: effects of the C-3 and C-5 stereochemistry of the pyrrolidinylthio side chain on antibacterial activities.

S. Sakuraba, H. Satō, H. Morishima, 2000, The Journal of antibiotics.

Diastereoselective synthesis of (2R,4R)-2-aryl-4-hydroxypyrrolidine: preparation of the side chain of novel carbapenem.

S. Sakuraba, M. Hirose, H. Morishima, 2001, Chemical & pharmaceutical bulletin.

Synthesis of J-111,347, a novel 1 beta-methylcarbapenem with broad-spectrum antibacterial activity.

S. Sakuraba, H. Morishima, N. Ohtake, 2000, Chemical & pharmaceutical bulletin.

Design Concepts for Developing Highly Efficient Chiral Bisphosphine Ligands in Rhodium-Catalyzed Asymmetric Hydrogenations

S. Sakuraba, K. Inoguchi, K. Achiwa, 1992 .

Synthesis of (β-N-Sulfonylaminoalkyl)phosphines and Their Use in Palladium-Mediated Asymmetric Synthesis

S. Sakuraba, K. Achiwa, Toshimi Okada, 1995 .

Interaction of naphthalene derivatives with lipids in membranes studied by the 1H-nuclear Overhauser effect and molecular dynamics simulation.

N. Matubayasi, S. Sakuraba, M. Shintani, 2012, Physical chemistry chemical physics : PCCP.

Efficient Asymmetric Hydrogenation of α-Amino Ketone Derivatives. A Highly Enantioselective Synthesis of Phenylephrine, Levamisole, Carnitine and Propranolol

S. Sakuraba, K. Achiwa, H. Takeda, 1995 .

Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex

J. Iwakiri, H. Kono, S. Sakuraba, 2022, PLoS Comput. Biol..

Modeling SARS-CoV-2 nsp1–5’-UTR complex via the extended ensemble simulations

J. Iwakiri, H. Kono, S. Sakuraba, 2021, bioRxiv.

Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters.

J. Iwakiri, K. Asai, Michiaki Hamada, 2020, Journal of chemical theory and computation.

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data

Michiaki Hamada, Kiyoshi Asai, Shun Sakuraba, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics.

N. Matubayasi, S. Sakuraba, M. Nakahara, 2011, The journal of physical chemistry. B.

H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation

Hidetoshi Kono, Jinzen Ikebe, Shun Sakuraba, 2016, PLoS Comput. Biol..

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities

Kiyoshi Asai, Ryota Mori, Junichi Iwakiri, 2018, BMC Bioinformatics.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

Nobuyuki Matubayasi, Akio Kitao, Kazuhiro Takemura, 2012, The Journal of chemical physics.

Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation

B. Garcia, H. Kono, B. Strahl, 2019, Nature Communications.

The N-terminal tails of histones H2A and H2B adopt two distinct conformations in the nucleosome with contact and reduced contact to DNA.

T. Umehara, H. Kono, H. Kurumizaka, 2021, Journal of molecular biology.

Identification of 2-aminobenzimidazoles as potent melanin-concentrating hormone 1-receptor (MCH1R) antagonists.

H. Iwaasa, S. Sakuraba, A. Kanatani, 2009, Bioorganic & medicinal chemistry letters.

Spotting the difference in molecular dynamics simulations of biomolecules.

Hidetoshi Kono, Shun Sakuraba, H. Kono, 2016, The Journal of chemical physics.

Molecular Binding Sites Are Located Near the Interface of Intrinsic Dynamics Domains (IDDs)

Aravind Chandrasekaran, Lee-Wei Yang, Hongchun Li, 2014, J. Chem. Inf. Model..

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.

HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks

H. Kono, S. Sakuraba, H. Taniguchi, 2022, Genes.

Role of the Photosystem II as an Environment on the Oxidation Free Energy of the Mn Cluster from S1 to S2.

S. Sakuraba, A. Morita, Hideaki Takahashi, 2019, The journal of physical chemistry. B.

A Novel 1β‐Methylcarbapenem, J‐111,225: Effects of the C‐3 and C‐5 Stereochemistry of the Pyrrolidinylthio Side Chain on Antibacterial Activities.

S. Sakuraba, H. Morishima, Koji Yamada, 2000 .

Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A.

T. Kameda, S. Sakuraba, R. Kitahara, 2017, Biophysical journal.

A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin

H. Yoshida, B. Mikami, A. Itoh, 2020, Nature Communications.

Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

H. Kono, S. Sakuraba, H. Ishida, 2019, Biophysics and physicobiology.

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA

Hidetoshi Kono, Hisashi Ishida, Shun Sakuraba, 2018, PLoS Comput. Biol..

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities

J. Iwakiri, K. Asai, S. Sakuraba, 2018, BMC Bioinformatics.

Interaction-component analysis of the hydration and urea effects on cytochrome c.

N. Matubayasi, S. Sakuraba, Y. Yamamori, 2016, The Journal of chemical physics.

Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions

Nobuyuki Matubayasi, Shun Sakuraba, N. Matubayasi, 2014, J. Comput. Chem..

Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations

Akio Kitao, Shun Sakuraba, A. Kitao, 2009, J. Comput. Chem..

Distribution-function approach to free energy computation.

N. Matubayasi, S. Sakuraba, 2011, The Journal of chemical physics.

Free-energy analysis of lysozyme–triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

Takeshi Ishikawa, Nobuyuki Matubayasi, Akio Kitao, 2013 .

H3 Histone Tail Structure within the Nucleosome and the Impact of the Acetylation

H. Kono, Jinzen Ikebe, S. Sakuraba, 2017 .