Spresso: an ultrafast compound pre-screening method based on compound decomposition. - Keisuke Yanagisawa; Shunta Komine; Shogo D. Suzuki; Masahito Ohue; Takashi Ishida 002; Yutaka Akiyama (Bioinform., 2017)

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. - Takanori Hayashi; Yuri Matsuzaki; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (BMC Bioinform., 2018)

Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques. - Takashi Tajimi; Naoki Wakui; Keisuke Yanagisawa; Yasushi Yoshikawa; Masahito Ohue; Yutaka Akiyama (BMC Bioinform., 2018)

Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm. - Keisuke Yanagisawa; Shunta Komine; Rikuto Kubota; Masahito Ohue; Yutaka Akiyama (Comput. Biol. Chem., 2018)

Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph. - Masahito Ohue; Ryota Ii; Keisuke Yanagisawa; Yutaka Akiyama (CoRR, 2019)

Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations. - Masatake Sugita; Satoshi Sugiyama; Takuya Fujie; Yasushi Yoshikawa; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 2021)

EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation. - Keisuke Yanagisawa; Yoshitaka Moriwaki; Tohru Terada; Kentaro Shimizu (J. Chem. Inf. Model., 2021)

Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning. - Jianan Li; Keisuke Yanagisawa; Yasushi Yoshikawa; Masahito Ohue; Yutaka Akiyama (Bioinform., 2022)

Solving Generalized Polyomino Puzzles Using the Ising Model. - Kazuki Takabatake; Keisuke Yanagisawa; Yutaka Akiyama (Entropy, 2022)

Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. - Masatake Sugita; Takuya Fujie; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 2022)

CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. - Jianan Li; Keisuke Yanagisawa; Masatake Sugita; Takuya Fujie; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 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)

CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation. - Jianan Li; Keisuke Yanagisawa; Yutaka Akiyama (Briefings Bioinform., 2024)

QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking. - Keisuke Yanagisawa; Takuya Fujie; Kazuki Takabatake; Yutaka Akiyama (Entropy, 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)