Yasuteru Shigeta

Center for Computational Sciences, university of tsukuba

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 3	2018

Other Publications

Article	Year
Distribution function in quantal cumulant dynamics. The Journal of chemical physics\| PubMed ID: 18447414	2008
First-principles molecular dynamics study on the atomistic behavior of His503 in bovine cytochrome c oxidase. Biochimica et biophysica acta\| PubMed ID: 21565155	2011
Theoretical insight into stereoselective reaction mechanisms of 2,4-pentanediol-tethered ketene-olefin [2 + 2] cycloaddition. The journal of physical chemistry. A\| PubMed ID: 22220552	2012
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method. Journal of computational chemistry\| PubMed ID: 25363340	2015
Simple, yet powerful methodologies for conformational sampling of proteins. Physical chemistry chemical physics : PCCP\| PubMed ID: 25659594	2015
Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin. Journal of computational chemistry\| PubMed ID: 25691321	2015
Theoretical study on reaction mechanisms of nitrite reduction by copper nitrite complexes: toward understanding and controlling possible mechanisms of copper nitrite reductase. The journal of physical chemistry. B\| PubMed ID: 25845517	2015
Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution. Journal of computational chemistry\| PubMed ID: 26611770	2016
Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study. The journal of physical chemistry. B\| PubMed ID: 27007978	2016
TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins. Journal of chemical theory and computation\| PubMed ID: 27070761	2016
Doubly N-Methylated Porphyrinoids. Organic letters\| PubMed ID: 27268126	2016
Ion-Pairing Crystal Polymorphs of Interlocked [2 + 1]-Type Receptor-Anion Complexes. The Journal of organic chemistry\| PubMed ID: 27526079	2016
Mutations affecting the internal equilibrium of the reaction catalyzed by 6-aminohexanoate-dimer hydrolase. FEBS letters\| PubMed ID: 27529542	2016
Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT study. Journal of computational chemistry\| PubMed ID: 27709623	2016
Molecular mechanisms of substrate specificities of uridinecytidine kinase. Biophysics and physicobiology\| PubMed ID: 27924260	2016
Cooperatively Interlocked [2+1]-Type π-System-Anion Complexes. Chemistry (Weinheim an der Bergstrasse, Germany)\| PubMed ID: 28087882	2017
Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins. Journal of chemical theory and computation\| PubMed ID: 28170260	2017
Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. Journal of computational chemistry\| PubMed ID: 28192630	2017
Large-scale QM/MM calculations of the CaMnO cluster in the S state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures. Faraday discussions\| PubMed ID: 28276543	2017
Theoretical analyses on a flipping mechanism of UV-induced DNA damage. Biophysics and physicobiology\| PubMed ID: 28409083	2016
Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical Dimer. Journal of the American Chemical Society\| PubMed ID: 28440644	2017
Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus. Journal of structural biology\| PubMed ID: 28456664	2017
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations. The journal of physical chemistry. B\| PubMed ID: 28489381	2017
Structural dissimilarity sampling with dynamically self-guiding selection. Journal of computational chemistry\| PubMed ID: 28558119	2017
Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior. Chemistry (Weinheim an der Bergstrasse, Germany)\| PubMed ID: 28696577	2017
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. Journal of computational chemistry\| PubMed ID: 28861895	2017
Assessment of Methodology and Chemical Group Dependences in the Calculation of the pK for Several Chemical Groups. Journal of chemical theory and computation\| PubMed ID: 28862859	2017
H-Aggregated π-Systems Based on Disulfide-Linked Dimers of Dipyrrolyldiketone Boron Complexes. The Journal of organic chemistry\| PubMed ID: 28960078	2017
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase. Journal of the American Chemical Society\| PubMed ID: 29037042	2017
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches. Journal of chemical information and modeling\| PubMed ID: 29111731	2017
The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational study. Biophysics and physicobiology\| PubMed ID: 29450111	2018
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα. Biochemical and biophysical research communications\| PubMed ID: 29567478	2018
Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study. Physical chemistry chemical physics : PCCP\| PubMed ID: 29577159	2018
On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins. Journal of chemical theory and computation\| PubMed ID: 29727581	2018
Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities. Nucleic acids research\| PubMed ID: 29762762	2018