Takatsugu Hirokawa

17 papers Journal 17

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Molecular simulation-based 3D structural construction of olfactory receptor with agonist binding. J. Comput. Aided Mol. Des. Takumi Hirao, Yusuke Ihara, Chiori Ijichi, Genki Kudo, Ryunosuke Yoshino, Takatsugu Hirokawa
2025	J	`jnl`	Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search. J. Chem. Inf. Model. Genki Kudo, Takumi Hirao, Ryuhei Harada, Yasuteru Shigeta, Takatsugu Hirokawa, Ryunosuke Yoshino
2025	J	`jnl`	CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis. J. Chem. Inf. Model. Jun Koseki, Chie Motono, Keisuke Yanagisawa, Genki Kudo, Ryunosuke Yoshino, Takatsugu Hirokawa, Kenichiro Imai
2024	J	`jnl`	Site Identification and Next Choice Protocol for Hit-to-Lead Optimization. J. Chem. Inf. Model. Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa
2023	J	`jnl`	AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics. J. Chem. Inf. Model. Genki Kudo, Keisuke Yanagisawa, Ryunosuke Yoshino, Takatsugu Hirokawa
2023	J	`jnl`	Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres. Bioinform. Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa
2021	J	`jnl`	MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts. Bioinform. Chie Motono, Shunsuke Yanagida, Miwa Sato, Takatsugu Hirokawa
2016	J	`jnl`	The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors. J. Chem. Inf. Model. Mitsugu Araki, Narutoshi Kamiya, Miwa Sato, Masahiko Nakatsui, Takatsugu Hirokawa, Yasushi Okuno
2015	J	`jnl`	Privacy-preserving search for chemical compound databases. BMC Bioinform. Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai
2014	J	`jnl`	Extended Template-Based Modeling and Evaluation Method Using Consensus of Binding Mode of GPCRs for Virtual Screening. J. Chem. Inf. Model. Miwa Sato, Takatsugu Hirokawa
2014	J	`jnl`	Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method. J. Chem. Inf. Model. Satoshi Yamasaki, Takatsugu Hirokawa, Kiyoshi Asai, Kazuhiko Fukui
2011	J	`jnl`	Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures - LERE-QSAR Analysis (IV). J. Chem. Inf. Model. Seiji Hitaoka, Hiroshi Matoba, Masataka Harada, Tatsusada Yoshida, Daisuke Tsuji, Takatsugu Hirokawa, Kohji Itoh, Hiroshi Chuman
2011	J	`jnl`	Discovery of Chemical Compound Groups with Common Structures by a Network Analysis Approach (Affinity Prediction Method). J. Chem. Inf. Model. Shigeru Saito, Takatsugu Hirokawa, Katsuhisa Horimoto
2010	J	`jnl`	Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes. BMC Bioinform. Nobuyuki Uchikoga, Takatsugu Hirokawa
2005	J	`jnl`	GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model. Nucleic Acids Res. Yukimitsu Yabuki, Takahiko Muramatsu, Takatsugu Hirokawa, Hidehito Mukai, Makiko Suwa
2002	J	`jnl`	Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces. Bioinform. Shigeki Mitaku, Takatsugu Hirokawa, Toshiyuki Tsuji
1998	J	`jnl`	SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinform. Takatsugu Hirokawa, Seah Boon-Chieng, Shigeki Mitaku