Keisuke Yanagisawa

15 papers Journal 15

Year	Rank	Type	Title / Venue / Authors
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`	CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation. Briefings Bioinform. Jianan Li, Keisuke Yanagisawa, Yutaka Akiyama
2024	J	`jnl`	QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking. Entropy Keisuke Yanagisawa, Takuya Fujie, Kazuki Takabatake, Yutaka Akiyama
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`	CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. J. Chem. Inf. Model. Jianan Li, Keisuke Yanagisawa, Masatake Sugita, Takuya Fujie, Masahito Ohue, Yutaka Akiyama
2022	J	`jnl`	Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. J. Chem. Inf. Model. Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
2022	J	`jnl`	Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning. Bioinform. Jianan Li, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama
2022	J	`jnl`	Solving Generalized Polyomino Puzzles Using the Ising Model. Entropy Kazuki Takabatake, Keisuke Yanagisawa, Yutaka Akiyama
2021	J	`jnl`	EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation. J. Chem. Inf. Model. Keisuke Yanagisawa, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu
2021	J	`jnl`	Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations. J. Chem. Inf. Model. Masatake Sugita, Satoshi Sugiyama, Takuya Fujie, Yasushi Yoshikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
2019	J	`jnl`	Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph. CoRR Masahito Ohue, Ryota Ii, Keisuke Yanagisawa, Yutaka Akiyama
2018	J	`jnl`	Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques. BMC Bioinform. Takashi Tajimi, Naoki Wakui, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama
2018	J	`jnl`	MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. BMC Bioinform. Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
2018	J	`jnl`	Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm. Comput. Biol. Chem. Keisuke Yanagisawa, Shunta Komine, Rikuto Kubota, Masahito Ohue, Yutaka Akiyama
2017	J	`jnl`	Spresso: an ultrafast compound pre-screening method based on compound decomposition. Bioinform. Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama