T. Ohyama

发表

Synthesis and the Origin of the Stability of Thiolate-Protected Au130 and Au187 Clusters.

Y. Negishi, T. Tsukuda, Chihiro Sakamoto, 2012, The journal of physical chemistry letters.

Specific interactions and binding energies between thermolysin and potent inhibitors: molecular simulations based on ab initio molecular orbital method.

Mahmud Tareq Hassan Khan, I. Sylte, N. Kurita, 2012, Journal of molecular graphics & modelling.

Structure-based analysis of the molecular recognitions between HIV-1 TAR-RNA and transcription factor nuclear factor-kappaB (NFkB).

R. Gambari, M. Borgatti, Mahmud Tareq Hassan Khan, 2012, Current topics in medicinal chemistry.

Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gene.

N. Sugimoto, T. Nishikata, D. Miyoshi, 2021, Chemical communications.

Effect of molecular crowding on the stability of RNA G-quadruplexes with various numbers of quartets and lengths of loops.

N. Sugimoto, Shuntaro Takahashi, Saki Matsumoto, 2020, Biochemistry.

Volumetric Strategy for Quantitatively Elucidating a Local Hydration Network around a G-Quadruplex.

N. Sugimoto, Sudipta Bhowmik, Shuntaro Takahashi, 2022, Analytical chemistry.

Effect of DNA modifications on the transition between canonical and non-canonical DNA structures in CpG islands during senescence

N. Sugimoto, Saki Matsumoto, H. Tateishi-Karimata, 2021, RSC advances.

New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures

N. Sugimoto, T. Muraoka, K. Kinbara, 2020, Molecules.

Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH–π interactions

N. Sugimoto, S. Nakano, J. Plavec, 2017, Nucleic acids research.

Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations

N. Sugimoto, J. Plavec, Shigenori Tanaka, 2018, Nucleic acids research.

Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition

N. Sugimoto, Saptarshi Ghosh, Shuntaro Takahashi, 2020, Nucleic acids research.

The effects of vitronectin on specific interactions between urokinase-type plasminogen activator and its receptor: ab initio molecular orbital calculations

N. Kurita, Eri Yoshikawa, Hiroshi Kobayashi, 2013 .

Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations

N. Kurita, K. Shimamura, T. Ohyama, 2019, Journal of Molecular Modeling.

Change in specific interactions between lactose repressor protein and DNA induced by ligand binding: molecular dynamics and molecular orbital calculations

N. Kurita, K. Shimamura, T. Ohyama, 2016 .

Specific interactions between lactose repressor protein and DNA affected by ligand binding: Ab initio molecular orbital calculations

Tatsuya Ohyama, Masato Hayakawa, Shin Nishikawa, 2011, J. Comput. Chem..

Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA.

N. Sugimoto, S. Nakano, D. Miyoshi, 2020, Biochemical and biophysical research communications.

Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins

Kaori Fukuzawa, T. Honma, C. Watanabe, 2021, J. Chem. Inf. Model..

Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions

N. Sugimoto, Saptarshi Ghosh, Shuntaro Takahashi, 2020, Proceedings of the National Academy of Sciences.

Correction to ‘Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition’

N. Sugimoto, Saptarshi Ghosh, Shuntaro Takahashi, 2021, Nucleic acids research.

Effect of Potassium Concentration on Triplex Stability under Molecular Crowding Conditions

N. Sugimoto, H. Tateishi-Karimata, T. Ohyama, 2020, Molecules.

141 Effect of ligand-binding on specific interactions between DNA and regulatory protein: molecular simulations based on MD and ab initio fragment MO methods

N. Kurita, K. Shimamura, T. Ohyama, 2015, Journal of Biomolecular Structure and Dynamics.

Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir Compared with Its Initial Screening Hit

Kaori Fukuzawa, C. Watanabe, Yoshio Okiyama, 2023, The journal of physical chemistry letters.

Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition.

N. Sugimoto, H. Tateishi-Karimata, T. Ohyama, 2018, Biochemical and biophysical research communications.

Ab initio fragment molecular orbital calculations on the specific interactions between human, mouse and rat PPARα and GW409544

T. Nakajima, N. Kurita, T. Ohyama, 2010 .

RNA-Capturing Microsphere Particles (R-CAMPs) for Optimization of Functional Aptamers.

N. Sugimoto, T. Endoh, T. Ohyama, 2019, Small.

Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions

N. Sugimoto, Shuntaro Takahashi, T. Endoh, 2023, Nucleic acids research.

Theranostic approach to specifically targeting the interloop region of BCL2 i-motif DNA by crystal violet

Shuntaro Takahashi, T. Ohyama, Sudipta Bhowmik, 2023, Scientific reports.

In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics.

J. Plavec, Shuntaro Takahashi, H. Tateishi-Karimata, 2023, Journal of the American Chemical Society.