Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations von Sugita, Masatake, Sugiyama, Satoshi, Fujie, Takuya, Yoshikawa, Yasushi, Yanagisawa, Keisuke, Ohue, Masahito, Akiyama, Yutaka

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CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides von Li, Jianan, Yanagisawa, Keisuke, Sugita, Masatake, Fujie, Takuya, Ohue, Masahito, Akiyama, Yutaka

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Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations von Sugita, Masatake, Fujie, Takuya, Yanagisawa, Keisuke, Ohue, Masahito, Akiyama, Yutaka

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

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Solving Generalized Polyomino Puzzles Using the Ising Model von Takabatake, Kazuki, Yanagisawa, Keisuke, Akiyama, Yutaka

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EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation von Yanagisawa, Keisuke, Moriwaki, Yoshitaka, Terada, Tohru, Shimizu, Kentaro

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MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions von Hayashi, Takanori, Matsuzaki, Yuri, Yanagisawa, Keisuke, Ohue, Masahito, Akiyama, Yutaka

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QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking von Yanagisawa, Keisuke, Fujie, Takuya, Takabatake, Kazuki, Akiyama, Yutaka

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Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques von Tajimi, Takashi, Wakui, Naoki, Yanagisawa, Keisuke, Yoshikawa, Yasushi, Ohue, Masahito, Akiyama, Yutaka

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Spresso: an ultrafast compound pre-screening method based on compound decomposition von Yanagisawa, Keisuke, Komine, Shunta, Suzuki, Shogo D, Ohue, Masahito, Ishida, Takashi, Akiyama, Yutaka

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Effective Protein–Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation von Yanagisawa, Keisuke, Kubota, Rikuto, Yoshikawa, Yasushi, Ohue, Masahito, Akiyama, Yutaka

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An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes von Chiba, Shuntaro, Ishida, Takashi, Ikeda, Kazuyoshi, Mochizuki, Masahiro, Teramoto, Reiji, Taguchi, Y-h., Iwadate, Mitsuo, Umeyama, Hideaki, Ramakrishnan, Chandrasekaran, Thangakani, A. Mary, Velmurugan, D., Gromiha, M. Michael, Okuno, Tatsuya, Kato, Koya, Minami, Shintaro, Chikenji, George, Suzuki, Shogo D., Yanagisawa, Keisuke, Shin, Woong-Hee, Kihara, Daisuke, Yamamoto, Kazuki Z., Moriwaki, Yoshitaka, Yasuo, Nobuaki, Yoshino, Ryunosuke, Zozulya, Sergey, Borysko, Petro, Stavniichuk, Roman, Honma, Teruki, Hirokawa, Takatsugu, Akiyama, Yutaka, Sekijima, Masakazu

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Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target von Chiba, Shuntaro, Ikeda, Kazuyoshi, Ishida, Takashi, Gromiha, M. Michael, Taguchi, Y-h., Iwadate, Mitsuo, Umeyama, Hideaki, Hsin, Kun-Yi, Kitano, Hiroaki, Yamamoto, Kazuki, Sugaya, Nobuyoshi, Kato, Koya, Okuno, Tatsuya, Chikenji, George, Mochizuki, Masahiro, Yasuo, Nobuaki, Yoshino, Ryunosuke, Yanagisawa, Keisuke, Ban, Tomohiro, Teramoto, Reiji, Ramakrishnan, Chandrasekaran, Thangakani, A. Mary, Velmurugan, D., Prathipati, Philip, Ito, Junichi, Tsuchiya, Yuko, Mizuguchi, Kenji, Honma, Teruki, Hirokawa, Takatsugu, Akiyama, Yutaka, Sekijima, Masakazu

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CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation von Li, Jianan, Yanagisawa, Keisuke, Akiyama, Yutaka

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Parallel metal–insulator–metal diode with an ultrathin spin-coated hydrogen silsesquioxane insulating layer von Akahane, Takashi, Ishii, Sho, Yanagisawa, Keisuke, Yin, You

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Megadock-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions von Ohue, Masahito, Hayashi, Takanori, Matsuzaki, Yuri, Yanagisawa, Keisuke, Akiyama, Yutaka

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Drug Clearance Pathway Prediction Based on Semi-supervised Learning von Yanagisawa, Keisuke, Ishida, Takashi, Akiyama, Yutaka

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AAp-MSMD: Amino Acid Preference Mapping on Protein–Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics von Kudo, Genki, Yanagisawa, Keisuke, Yoshino, Ryunosuke, Hirokawa, Takatsugu

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Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes von Yanagisawa, Keisuke, Yoshino, Ryunosuke, Kudo, Genki, Hirokawa, Takatsugu

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QEX: target-specific druglikeness filter enhances ligand-based virtual screening von Mochizuki, Masahiro, Suzuki, Shogo D., Yanagisawa, Keisuke, Ohue, Masahito, Akiyama, Yutaka

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