KINJO, Akira - Osaka University - Department of Chemistry

个人简介

2009-present Associate Professor, Institute for Protein Research, Osaka University (current position) 2008-present Visiting Associate Professor, Database Center for Life Science, Research Organization of Information and Systems. 2006-2008 Visiting Associate Professor, Institute for Protein Research, Osaka University 2003-2006 Assistant Professor, National Institute of Genetics 2001-2003 Postdoctoral Fellow in Prof. Shoji Takada's lab (Kobe University) Education 1998-2001 Ph.D. in Genetics, The Graduate University for Advanced Studies 1996-1998 M.Sc. in Chemistry, Kyoto University 1993-1996 Drop-out, Faculty of Science, Kyoto University 1990-1991 San Dieguito High School (The President's Youth Exchange Initiative) 1989-1993 Graduated from Kyuyo High School in Okinawa, Japan

研究领域

Our laboratory, Laboratory of Protein Informatics, is engaged in the protein informatics researches by developing the international protein structural databases and the structural bioinformatics covering molecular modeling and design. We also perform large scale simulation calculations by parallel computers to examine free energy landscapes and biochemical functions of biomolecular systems with molecular dynamics and quantum chemistry simulations. Protein structure determination by X-ray crystallography is also our aim to understand the structure-function relationships. Research Activities Laboratory of Protein Informatics are engaged in the following protein informatics researches: Development and maintenance of international protein structural databases (PDBj) and structural bioinformatics covering molecular modeling and design. Development of new databases and Web services: eF-site, for protein surface geometry with the physicochemical properties; PreDs, for prediction of the putative double-stranded DNA binding sites of proteins based on the protein molecular surface features; and HINT, Homologous Interaction Database. Structural bioinformatics studies, focusing on protein-protein interactions. Large scale simulation calculations by parallel computers to examine free energy landscapes of biomolecular systems with the hybrid QM (Quantum mechanics) / MM (Molecular mechanics) method for analysis of biochemical reactions. Protein structure determination by X-ray crystallography and protein function analysis.

近期论文

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Implementation of Linked Data in the Life Sciences at BioHackathon 2011. Aoki-Kinoshita KF, Kinjo AR, Morita M, Igarashi Y, Chen Y, Shigemoto Y, Fujisawa T, Akune Y, Katoda T, Kokubu A, Mori T, Nakao M, Kawashima S, Okamoto S, Katayama T, Ogishima S. Journal of Biomedical Semantics 6:3 (2015) [DOI:10.1186/2041-1480-6-3] Cooperation between phenotypic plasticity and genetic mutations can account for the cumulative selection in evolution. Nishikawa K, Kinjo AR. BIOPHYSICS 10:99-108 (2014) [DOI:10.2142/biophysics.10.99] Specific non-local interactions are not necessary for recovering native protein dynamics. Dasgupta B, Kasahara K, Kamiya N, Nakamura H, Kinjo AR. PLoS One 9:e91347 (2014) [PubMed] [DOI:10.1371/journal.pone.0091347] Rigid-body motions of interacting proteins dominate multi-specific binding of Ubiquitin in a shape-dependent manner. Dasgupta B, Nakamura H, Kinjo AR. Proteins: Structure, Function, and Bioinformatics 82:77-89 (2014) [PubMed] [DOI:10.1002/prot.24371] Exhaustive comparison and classification of ligand-binding surfaces in proteins. Murakami Y, Kinoshita K, Kinjo AR, Nakamura H. Protein Science 22:1379-1391 (2013) [PubMed] [DOI:10.1002/pro.2329] The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies. Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock P, Eriksson T, Gordon P, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos R, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T. Journal of Biomedical Semantics 4:6 (2013) [PubMed] [DOI:10.1186/2041-1480-4-6] Counterbalance of ligand- and self-coupled motions characterizes multi-specificity of Ubiquitin. Dasgupta B, Nakamura H, Kinjo AR. Protein Science 22:168-178 (2013) [PubMed] [DOI:10.1002/pro.2195] Functional structural motifs for protein-ligand, protein-protein and protein-nucleic acid interactions and their connection to supersecondary structures. Kinjo AR, Nakamura H. Methods in Molecular Biology 932:295-315 (2013) [PubMed] [DOI:10.1007/978-1-62703-065-6_18] GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. Kinjo AR, Nakamura H. BIOPHYSICS 8:79-94 (2012) [DOI:10.2142/biophysics.8.79] Composite structural motifs of binding sites for delineating biological functions of proteins. Kinjo AR, Nakamura H. PLoS One 7:e31437 (2012) [PubMed] [arXiv:1107.3278] [DOI:10.1371/journal.pone.0031437] Protein Data Bank Japan (PDBj): Maintaining a structural data archive and Resource Description Framework format. Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudo T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H. Nucleic Acids Research 40:D453-D460 (2012) [PubMed] [DOI:10.1093/nar/gkr811] Functional characterization of protein domains common to animal viruses and mouse. Kinjo AR, Kumagai Y, Dinh H, Takeuchi O, Standley DM. BMC Genomics 12:S21 (2011) [PubMed] [DOI:10.1186/1471-2164-12-S3-S21] The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJP, Fernandez JM, Fujisawa T, Gordon PMK, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T. Journal of Biomedical Semantics 2:4 (2011) [PubMed] [DOI:10.1186/2041-1480-2-4] Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners. Dasgupta B, Nakamura H, Kinjo AR. Journal of Molecular Biology 411:713-727 (2011) [PubMed] [DOI:10.1016/j.jmb.2011.06.027] Bridging the gap between single-template and fragment based protein structure modeling using Spanner. Lis M, Kim T, Sarmiento J, Kuroda D, Dinh H, Kinjo AR, Amada K, Devadas S, Nakamura H, Standley DM. Immunome Research 7:1-8 (2011) [PubMed] [http://immunome-research.net/journal/index.php/immunome/article/view/5] PDBj Mine: Design and implementation of relational database interface for Protein Data Bank Japan. Kinjo AR, Yamashita R, Nakamura H. Database 2010:baq021 (2010) [PubMed] [DOI:10.1093/database/BAQ021] The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun H-W, Aerts J, Aranda B, Barboza LH, Bonnal RJP, Bruskiewich R, Bryne JC, Fernandez JM, Funahashi A, Gordon PMK, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T. Journal of Biomedical Semantics 1:8 (2010) [PubMed] [DOI:10.1186/2041-1480-1-8] Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study. Kinjo AR, Nakamura H. Journal of Molecular Biology 399:526-540 (2010) [PubMed] [DOI:10.1016/j.jmb.2010.04.028] SeSAW: balancing sequence and structural information in protein functional mapping. Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H. Bioinformatics 26:1258-1259 (2010) [PubMed] [DOI:10.1093/bioinformatics/btq116] Profile conditional random fields for modeling protein families with structural information. Kinjo AR. BIOPHYSICS 5:37-44 (2009) [arXiv:0904.2627] [DOI:10.2142/biophysics.5.37]"