Computational Drug Discovery and Design

41  articles.  
* There may be some overlapped articles listed due to the difference of format.

  1. Ishitani, R; Takemoto, M; Tomii, K: Protein ligand binding site prediction using graph transformer neural network PLOS ONE. 2024.08; 19 (8): e0308425. ( PubMed , DOI )

  1. Molecular Design Method Using a Reversible Tree Representation of Chemical Compounds and Deep Reinforcement Learning. 2022.09; 62 (17): 4032-4048. ( PubMed , DOI )

  2. Towards universal neural network potential for material discovery applicable to arbitrary combination of 45 elements. 2022.05; 13 (1): 2991. ( PubMed , DOI )

  3. Lateral access mechanism of LPA receptor probed by molecular dynamics simulation. 2022; 17 (2): e0263296. ( PubMed , DOI )

  1. Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. 2021.03; 10 ( PubMed , DOI )

  1. Structural biology of the multidrug and toxic compound extrusion superfamily transporters. 2020.12; 1862 (12): 183154. ( PubMed , DOI )

  2. Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation. 2020.05; 3 (1): 240. ( PubMed , DOI )

  3. Identification of Potent In Vivo Autotaxin Inhibitors that Bind to Both Hydrophobic Pockets and Channels in the Catalytic Domain. 2020.03; 63 (6): 3188-3204. ( PubMed , DOI )

  4. Author Correction: Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. 2020.02; 578 (7794): E19. ( PubMed , DOI )

  5. Crystal structure of Drosophila Piwi. 2020.02; 11 (1): 858. ( PubMed , DOI )

  1. Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc. 2019.06; 26 (6): 510-517. ( PubMed , DOI )

  2. Structural basis for oligomerization of the prokaryotic peptide transporter PepTSo2. 2019.05; 75 (Pt 5): 348-358. ( PubMed , DOI )

  3. Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9. 2019.04; 10 (1): 1968. ( PubMed , DOI )

  4. Crystal structure of plant vacuolar iron transporter VIT1. 2019.03; 5 (3): 308-315. ( PubMed , DOI )

  5. Structural Basis of H+-Dependent Conformational Change in a Bacterial MATE Transporter. 2019.02; 27 (2): 293-301. ( PubMed , DOI )

  6. Cap-specific terminal N 6-methylation of RNA by an RNA polymerase II-associated methyltransferase. 2019.01; 363 (6423): ( PubMed , DOI )

  1. Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex. 2018.12; 74 (Pt 12): 810-816. ( PubMed , DOI )

  2. Vibrational and Molecular Properties of Mg2+ Binding and Ion Selectivity in the Magnesium Channel MgtE. 2018.10; 122 (42): 9681-9696. ( PubMed , DOI )

  3. An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin. 2018.10; 115 (7): 1281-1291. ( PubMed , DOI )

  4. Kato K, Nishimasu H, Oikawa D, Hirano S, Hirano H, Kasuya G, Ishitani R, Tokunaga F, Nureki O: Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1. Nature communications. 2018.10; 9 (1): 4424. ( PubMed , DOI )

  5. Engineered CRISPR-Cas9 nuclease with expanded targeting space. 2018.09; 361 (6408): 1259-1262. ( PubMed , DOI )

  6. Free Energy Landscape for the Entire Transport Cycle of Triose-Phosphate/Phosphate Translocator. 2018.09; 26 (9): 1284-1296. ( PubMed , DOI )

  7. Cryo-EM structures of the human volume-regulated anion channel LRRC8. 2018.09; 25 (9): 797-804. ( PubMed , DOI )

  8. Functional roles of Mg2+ binding sites in ion-dependent gating of a Mg2+ channel, MgtE, revealed by solution NMR. 2018.04; 7 ( PubMed , DOI )

  1. Structural basis for xenobiotic extrusion by eukaryotic MATE transporter. 2017.11; 8 (1): 1633. ( PubMed , DOI )

  2. Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel. 2017.10; 8 (1): 876. ( PubMed , DOI )

  3. Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity. 2017.10; 3 (10): 825-832. ( PubMed , DOI )

  4. Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA6. 2017.08; 548 (7667): 356-360. ( PubMed , DOI )

  5. Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. 2017.08; 67 (4): 633-645. ( PubMed , DOI )

  6. ATP-dependent modulation of MgtE in Mg2+ homeostasis. 2017.07; 8 (1): 148. ( PubMed , DOI )

  7. Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1. 2017.07; 67 (1): 139-147. ( PubMed , DOI )

  8. Kato Kazuki, Omura Hiroki, Ishitani Ryuichiro, Nureki Osamu: Cyclic GMP-AMP as an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA. Annu Rev Biochem. 2017.06; 86 541-566. ( PubMed , DOI )

  9. Structural insights into the nucleotide base specificity of P2X receptors. 2017.03; 7 45208. ( PubMed , DOI )

  10. Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems. 2017.03; 65 (6): 1109-1121. ( PubMed , DOI )

  11. Correction: Breakpoint Cluster Region-Mediated Inflammation Is Dependent on Casein Kinase II. 2017.01; 198 (2): 971. ( PubMed , DOI )

  1. Ishitani Ryuuitirou: Deep Learning for Drug Discovery Proceedings for Annual Meeting of The Japanese Pharmacological Society. 2019; 92 3-CS4-3. ( DOI )

  1. 田中良樹, 氏原一哉, 坂井直樹, 山田悠介, 武本瑞貴, 森脇寛智, 佐藤匡史, STANFIELD Joshua Kyle, 梅本直, 平田邦生, 引田理英, 石谷隆一郎, 加藤龍一, 千田俊哉, 山本雅貴, 力丸健太郎, 西ヶ谷有輝: Structure Based Discovery of Novel ALS Inhibitors 日本農薬学会大会講演要旨集(CD-ROM). 2023; 48th

  1. 田中良樹, 氏原一哉, 坂井直樹, 武本瑞貴, 森脇寛智, 佐藤匡史, STANFIELD JK, 平田邦生, 竹下浩平, 石谷隆一郎, 山本雅貴, 力丸健太郎, 西ヶ谷有輝: Structure Based Discovery of Novel ALS Inhibitors 日本農薬学会大会講演要旨集(CD-ROM). 2022; 47th

  1. 小野田浩宜, 石谷隆一郎, 仙石徹, 森脇由隆: The Impact of AlphaFold on Molecular Biology 日本分子生物学会年会プログラム・要旨集(Web). 2021; 44th

  2. 石谷隆一郎, 石谷隆一郎, 武本瑞貴: AlphaFold from the perspective of structural biology and deep learning 日本分子生物学会年会プログラム・要旨集(Web). 2021; 44th

  1. Taniguchi Reiya, Inoue Asuka, Sayama Misa, Yamashita Keitaro, Hirata Kunio, Yoshida Masahito, Nakada-Nakura Yoshiko, Otani Yuko, Kato Hideaki, Nishizawa Tomohiro, Doi Takayuki, Ohwada Tomohiko, Ishitani Ryuichiro, Aoki Junken, Nureki Osamu: Toward Structural Understanding of Ligand Recognition by Lysophosphatidic Acid Receptor Lpa6 PROTEIN SCIENCE. 2018.11; 27 235-236.

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