Home＞Research＞Team＞in-silico Drug Design Team＞Mission
Molecular simulation team
Mission
Leader Takatsugu Hirokawa
Research Topics
- ■Protein structure modeling, protein-ligand docking and protein-protein interaction analysis for the drug target proteins.
- ■Structure-based drug design and chemoinformatics.
- ■Development of high throughput protein modeling system
- ■Molecular dynamics simulations of protein folding and amyloid peptide aggregation.
- ■In silico screening for drug discovery in collaboration with pharmaceutical companies and the chemical biology project.
Papers List
| 2015 |
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NovelpH-dependent regulation of human cytosolic sialidase2 (NEU2) activities by siastatin B and structural prediction of NEU2/siastatin B complex Biochem. Biophys. Rep., 2015, 4, 234-242. Rahman M.M, Hirokawa T, Tsuji D, Tsukimoto J, Hitaoka S, Yoshida T, Chuman H, Itoh K |
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Privacy-preserving search for chemical compound databases BMC Bioinformatics, 2015, 16 Suppl 18, S6. Shimizu K, Nuida K, Arai H, Mitsunari S, Attrapadung N, Hamada M, Tsuda K, Hirokawa T, Sakuma J, Hanaoka G, Asai K |
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Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target Sci. Rep., 2015, 5, 17209 Chiba S, Ikeda K, Ishida T, Gromiha MM, Taguchi YH, Iwadate M, Umeyama H, Hsin KY, Kitano H, Yamamoto K, Sugaya N, Kato K, Okuno T, Chikenji G, Mochizuki M, Yasuo N, Yoshino R, Yanagisawa K, Ban T, Teramoto R, Ramakrishnan C, Thangakani AM, Velmurugan D, Prathipati P, Ito J, Tsuchiya Y, Mizuguchi K, Honma T, Hirokawa T, Akiyama Y, Sekijima M. |
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Design and synthesis of a berberine dimer: a fluorescent ligand with high affinity towards G-quadruplexes Chemistry, 2015, 21, 14519-14528. Tera M, Hirokawa T, Okabe S, Sugahara K, Seimiya H, Shimamoto K |
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Site-specific Interaction Mapping of Phosphorylated Ubiquitin to Uncover Parkin Activation J. Biol. Chem., 2015, 290, 25199-25211. Yamano K, Queliconi BB, Koyano F, Saeki Y, Hirokawa T, Tanaka K, Matsuda N |
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Relationship between Human Evolution and Neurally Mediated Syncope Disclosed by the Polymorphic Sites of the Adrenergic Receptor Gene α2B-AR PLoS One, 2015, 10(4), e0120788. Komiyama T, Hirokawa T, Sato K, Oka A, Kamiguchi H, Nagata E, Sakura H, Otsuka K, Kobayashi H |
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Molecular dynamics simulation and experimental verification of the interaction between cyclin T1 and HIV-1 Tat proteins PLoS One, 2015, 10(3), e0119451. Asamitsu K, Hirokawa T, Hibi Y, Okamoto T. |
| 2012 |
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Trichostatin Analogues JBIR-109, JBIR-110, and JBIR-111 from the Marine Sponge-Derived Streptomyces sp. RM72. Journal of natural products, 75(2) pp.285-9(2012). Hosoya, T., Hirokawa, T., Takagi, M., Shin-Ya, K. |
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Cyclopropane-based stereochemical diversity-oriented conformational restriction strategy: histamine H3 and/or H4 receptor ligands with the 2,3-methanobutane backbone. Organic & Biomolecular Chemistry, 10(4) pp.736-745(2012). Watanabe, M., Kobayashi, T., Hirokawa, T., Yoshida, A., Ito, Y., Yamada, S., Orimoto, N., Yamasaki, Y., Arisawa, M., Shuto, S. |
| 2011 |
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Computational analysis of ligand recognition mechanisms by prostaglandin E2 (subtype 2) and D2 receptors." Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 130, pp.1131-1143(2011). Daiyasu, H., Hirokawa, T., Kamiya, N., Toh, H. |
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Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes. BMC Bioinformatics, 11, pp.236(2010). Uchikoga, N., Hirokawa, T. |