Narutoshi Kamiya - researchr alias

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Viewing Publication 1 - 13 from 13

2026

Elucidating Ligand Charge Effects in MR1 Cell-Surface Translocation Using Molecular SimulationsToshiki Fujii, Mitsugu Araki, Shigeyuki Matsumoto, Biao Ma, Takao Otsuka, Gert-Jan Bekker, Narutoshi Kamiya, Hiroaki Ohno, Shinsuke Inuki, Yasushi Okuno. jcisd, 66(4):2211-2219, 2026. [doi]

2024

Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic DockingGert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya. jcisd, 64(10):4158-4167, 2024. [doi]

2021

Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic DockingGert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya. jcisd, 61(10):5161-5171, 2021. [doi]

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover EquationKei Moritsugu, Koh Takeuchi, Narutoshi Kamiya, Junichi Higo, Isao Yasumatsu, Yoshifumi Fukunishi, Ikuo Fukuda. jcisd, 61(4):1921-1930, 2021. [doi]

2020

Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic dockingGert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya. jcc, 41(17):1606-1615, 2020. [doi]

Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational SamplingJunichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura. jcisd, 60(10):4867-4880, 2020. [doi]

Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction PatternsAtsushi Tokuhisa, Ryo Kanada, Shuntaro Chiba, Kei Terayama, Yuta Isaka, Biao Ma, Narutoshi Kamiya, Yasushi Okuno. jcisd, 60(6):2803-2818, 2020. [doi]

2018

Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation ApproachMitsugu Araki, Hiroaki Iwata, Biao Ma, Atsuto Fujita, Kei Terayama, Yukari Sagae, Fumie Ono, Koji Tsuda, Narutoshi Kamiya, Yasushi Okuno. jcc, 39(32):2679-2689, 2018. [doi]

2016

The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their InhibitorsMitsugu Araki, Narutoshi Kamiya, Miwa Sato, Masahiko Nakatsui, Takatsugu Hirokawa, Yasushi Okuno. jcisd, 56(12):2445-2456, 2016. [doi]

Model Building of Antibody-Antigen Complex Structures Using GBSA ScoresNoriko Shimba, Narutoshi Kamiya, Haruki Nakamura. jcisd, 56(10):2005-2012, 2016. [doi]

2011

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in waterJinzen Ikebe, Koji Umezawa, Narutoshi Kamiya, Takanori Sugihara, Yasushige Yonezawa, Yu Takano, Haruki Nakamura, Junichi Higo. jcc, 32(7):1286-1297, 2011. [doi]

2009

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systemsGota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, Makoto Taiji, Ryutaro Himeno, Haruki Nakamura, Yasushige Yonezawa. jcc, 30(1):110-118, 2009. [doi]

2001

Repeated-annealing sampling combined with multicanonical algorithm for conformational sampling of bio-moleculesNarutoshi Kamiya, Junichi Higo. jcc, 22(10):1098-1106, 2001. [doi]

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