SOSUI: classification and secondary structure prediction system for membrane proteins. - Takatsugu Hirokawa; Seah Boon-Chieng; Shigeki Mitaku (Bioinform., 1998)

Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces. - Shigeki Mitaku; Takatsugu Hirokawa; Toshiyuki Tsuji (Bioinform., 2002)

GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model. - Yukimitsu Yabuki; Takahiko Muramatsu; Takatsugu Hirokawa; Hidehito Mukai; Makiko Suwa (Nucleic Acids Res., 2005)

Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes. - Nobuyuki Uchikoga; Takatsugu Hirokawa (BMC Bioinform., 2010)

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). - Seiji Hitaoka; Hiroshi Matoba; Masataka Harada; Tatsusada Yoshida; Daisuke Tsuji; Takatsugu Hirokawa; Kohji Itoh; Hiroshi Chuman (J. Chem. Inf. Model., 2011)

Discovery of Chemical Compound Groups with Common Structures by a Network Analysis Approach (Affinity Prediction Method). - Shigeru Saito; Takatsugu Hirokawa; Katsuhisa Horimoto (J. Chem. Inf. Model., 2011)

Extended Template-Based Modeling and Evaluation Method Using Consensus of Binding Mode of GPCRs for Virtual Screening. - Miwa Sato; Takatsugu Hirokawa (J. Chem. Inf. Model., 2014)

Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method. - Satoshi Yamasaki; Takatsugu Hirokawa; Kiyoshi Asai; Kazuhiko Fukui (J. Chem. Inf. Model., 2014)

Privacy-preserving search for chemical compound databases. - Kana Shimizu; Koji Nuida; Hiromi Arai; Shigeo Mitsunari; Nuttapong Attrapadung; Michiaki Hamada; Koji Tsuda; Takatsugu Hirokawa; Jun Sakuma; Goichiro Hanaoka; Kiyoshi Asai (BMC Bioinform., 2015)

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)

MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts. - Chie Motono; Shunsuke Yanagida; Miwa Sato; Takatsugu Hirokawa (Bioinform., 2021)

Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres. - Genki Kudo; Takumi Hirao; Ryunosuke Yoshino; Yasuteru Shigeta; Takatsugu Hirokawa (Bioinform., 2023)

AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics. - Genki Kudo; Keisuke Yanagisawa; Ryunosuke Yoshino; Takatsugu Hirokawa (J. Chem. Inf. Model., 2023)

Site Identification and Next Choice Protocol for Hit-to-Lead Optimization. - Genki Kudo; Takumi Hirao; Ryunosuke Yoshino; Yasuteru Shigeta; Takatsugu Hirokawa (J. Chem. Inf. Model., 2024)

CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis. - Jun Koseki; Chie Motono; Keisuke Yanagisawa; Genki Kudo; Ryunosuke Yoshino; Takatsugu Hirokawa; Kenichiro Imai (J. Chem. Inf. Model., 2025)

Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search. - Genki Kudo; Takumi Hirao; Ryuhei Harada; Yasuteru Shigeta; Takatsugu Hirokawa; Ryunosuke Yoshino (J. Chem. Inf. Model., 2025)