Repeated-annealing sampling combined with multicanonical algorithm for conformational sampling of bio-molecules. - Narutoshi Kamiya; Junichi Higo (J. Comput. Chem., 2001)

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. - Gota Kikugawa; Rossen Apostolov; Narutoshi Kamiya; Makoto Taiji; Ryutaro Himeno; Haruki Nakamura; Yasushige Yonezawa (J. Comput. Chem., 2009)

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. - Jinzen Ikebe; Koji Umezawa; Narutoshi Kamiya; Takanori Sugihara; Yasushige Yonezawa; Yu Takano; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2011)

The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors. - Mitsugu Araki; Narutoshi Kamiya; Miwa Sato; Masahiko Nakatsui; Takatsugu Hirokawa; Yasushi Okuno (J. Chem. Inf. Model., 2016)

Model Building of Antibody-Antigen Complex Structures Using GBSA Scores. - Noriko Shimba; Narutoshi Kamiya; Haruki Nakamura (J. Chem. Inf. Model., 2016)

Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach. - Mitsugu Araki; Hiroaki Iwata; Biao Ma; Atsuto Fujita; Kei Terayama; Yukari Sagae; Fumie Ono; Koji Tsuda; Narutoshi Kamiya; Yasushi Okuno (J. Comput. Chem., 2018)

Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking. - Gert-Jan Bekker; Mitsugu Araki; Kanji Oshima; Yasushi Okuno; Narutoshi Kamiya (J. Comput. Chem., 2020)

Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. - Junichi Higo; Takeshi Kawabata; Ayumi Kusaka; Kota Kasahara; Narutoshi Kamiya; Ikuo Fukuda; Kentaro Mori; Yutaka Hata; Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2020)

Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns. - Atsushi Tokuhisa; Ryo Kanada; Shuntaro Chiba; Kei Terayama; Yuta Isaka; Biao Ma; Narutoshi Kamiya; Yasushi Okuno (J. Chem. Inf. Model., 2020)

Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking. - Gert-Jan Bekker; Mitsugu Araki; Kanji Oshima; Yasushi Okuno; Narutoshi Kamiya (J. Chem. Inf. Model., 2021)

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. - Kei Moritsugu; Koh Takeuchi; Narutoshi Kamiya; Junichi Higo; Isao Yasumatsu; Yoshifumi Fukunishi; Ikuo Fukuda (J. Chem. Inf. Model., 2021)

Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. - Gert-Jan Bekker; Kanji Oshima; Mitsugu Araki; Yasushi Okuno; Narutoshi Kamiya (J. Chem. Inf. Model., 2024)