List of Publications

Original Papers

33. GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.
    Kinjo AR, Nakamura H.
    BIOPHYSICS in press:(2012)
32. 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 in press:(2012)
31. 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]
30. 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]
29. 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]
28. 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]
27. 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]
26. 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]
25. 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]
24. 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]
23. 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]
22. 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]
21. 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]
20. Comprehensive structural classification of ligand binding motifs in proteins.
    Kinjo AR, Nakamura H.
    Structure 17:234-246 (2009) [PubMed] [arXiv:0810.1327] [DOI:10.1016/j.str.2008.11.009]
19. Structure-based functional annotation of protein sequences guided by comparative models.
    Standley DM, Kinjo AR, Lis M, van der Giezen M, Nakamura H.
    Lecture Notes in Operations Research (The Second International Symposium on Optimization and Systems Biology) 9:395-403 (2008) [http://www.aporc.org/LNOR/9/OSB2008F50.pdf]
18. Protein structure databases with new web services for structural biology and biomedical research.
    Standley DM, Kinjo AR, Kinoshita K, Nakamura H.
    Briefings in Bioinformatics 9:276-285 (2008) [PubMed] [DOI:10.1093/bib/bbn015]
17. Properties of contact matrices induced by pairwise interactions in proteins.
    Miyazawa S, Kinjo AR.
    Physical Review E 77:051910 (2008) [PubMed] [arXiv:0801.0365] [DOI:10.1103/PhysRevE.77.051910]
16. Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices.
    Kinjo AR, Nakamura H.
    PLoS One 3:e1963 (2008) [PubMed] [arXiv:0711.1010] [DOI:10.1371/journal.pone.0001963]
15. On the optimal contact potential of proteins.
    Kinjo AR, Miyazawa S.
    Chemical Physics Letters 451:132-135 (2008) [arXiv:0709.0346] [DOI:10.1016/j.cplett.2007.12.005]
14. Similarity search for local protein structures at atomic resolution by exploiting a database management system.
    Kinjo AR, Nakamura H.
    BIOPHYSICS 3:75-84 (2007) [arXiv:0711.1012] [DOI:10.2142/biophysics.3.75]
13. Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins.
    Nagasima T, Kinjo AR, Mitsui T, Nishikawa K.
    Physical Review E 75:066706 (2007) [PubMed] [arXiv:0704.3365] [DOI:10.1103/PhysRevE.75.066706]
12. CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks.
    Kinjo AR, Nishikawa K.
    BMC Bioinformatics 7:401 (2006) [PubMed] [arXiv:q-bio/0604013] [DOI:10.1186/1471-2105-7-401]
11. Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation.
    Minezaki Y, Homma K, Kinjo AR, Nishikawa K.
    Journal of Molecular Biology 359:1137-1149 (2006) [PubMed] [DOI:10.1016/j.jmb.2006.04.016]
10. Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks.
    Kinjo AR, Nishikawa K.
    BIOPHYSICS 1:67-74 (2005) [arXiv:q-bio.BM/0503032] [DOI:10.2142/biophysics.1.67]
9. Recoverable one-dimensional encoding of three-dimensional protein structures.
   Kinjo AR, Nishikawa K.
   Bioinformatics 21:2167-2170 (2005) [PubMed] [arXiv:q-bio.BM/0501005] [DOI:10.1093/bioinformatics/bti330]
8. Predicting absolute contact numbers of native protein structure from amino acid sequence.
   Kinjo AR, Horimoto K, Nishikawa K.
   Proteins: Structure, Function, and Bioinformatics 58:158-165 (2005) [PubMed] [DOI:10.1002/prot.20300]
7. Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins.
   Kinjo AR, Nishikawa K.
   Bioinformatics 20:2504-2508 (2004) [PubMed] [Supplement] [DOI:10.1093/bioinformatics/bth297]
6. Competition between protein folding and aggregation with molecular chaperones in crowded solutions: Insight from mesoscopic simulations.
   Kinjo AR, Takada S.
   Biophysical Journal 85:3521-3531 (2003) [PubMed] [DOI:doi:10.1016/S0006-3495(03)74772-9]
5. Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: Dynamics.
   Kinjo AR, Takada S.
   Physical Review E 66:051902 (2002) [PubMed] [DOI:10.1103/PhysRevE.66.051902]
4. Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: Statics.
   Kinjo AR, Takada S.
   Physical Review E 66:031911 (2002) [PubMed] [DOI:10.1103/PhysRevE.66.031911]
3. Comparison of energy components of proteins from thermophilic and mesophilic organisms.
   Kinjo AR, Nishikawa K.
   European Biophysics Journal 30:378-384 (2001) [PubMed] [DOI:10.1007/s002490100161]
2. Physicochemical evaluation of protein folds predicted by threading.
   Kinjo AR, Kidera A, Nakamura H, Nishikawa K.
   European Biophysics Journal 30:1-10 (2001) [PubMed] [DOI:10.1007/s002490000111]
1. Cooperative approach for the protein fold recognition.
   Ota M, Kawabata T, Kinjo AR, Nishikawa K.
   Proteins: Structure, Function, and Genetics Suppl 3:126-132 (1999) [PubMed] [DOI:10.1002/(SICI)1097-0134(1999)37:3+<126::AID-PROT17>3.0.CO;2-8]

Others

10. タンパク質の立体構造データベース
    金城玲．
    実験医学増刊『使えるデータベース・ウェブツール-日本発のデータベース戦略からゲノム・疾患情報の有効活用まで』, 29:2432-2437 (2011).
9. データを解釈する者は誰か -和田昭允先生に応えて
   金城玲.
   生物物理, 50:166-167 (2010).[DOI:10.2142/biophys.50.166]
8. 蛋白質の高精度２次構造予測
   金城玲.
   蛋白質 核酸 酵素,52(1):50-56 (2007). In Japanese.
7. データベース解説：PDB/GTOP
   金城玲, 西川建.
   細胞工学, 25(3):293-297 (2006). In Japanese.
6. タンパク質の立体構造情報はどのようにアミノ酸配列に埋めこまれているか？
   金城玲.
   生物物理, 46:37-40 (2006).[DOI:10.2142/biophys.46.37] (in Japanese).
5. 蛋白質の２次構造予測
   金城玲.
   In バイオインフォマティクス事典 (2006), 共立出版. In Japanese.
4. タンパク質の構造予測
   金城玲, 西川建.
   In タンパク質科学ー構造・物性・機能, (2005), 化学同人. In Japanese.
3. タンパク質構造へのアプローチ
   金城玲.
   In DDBJ の利用法, Gojobori, T. and Sugawara, H. (eds.), 共立出版., (2005) In Japanese.
2. PDB (蛋白質立体構造座標データベース)
   金城玲.
   In バイオデータベース利用法, Kanehisa, M et al. (eds.), 学進出版. (2005) In Japanese.
1. 自滅する生物情報学者?
   金城玲.
   DDBJ メールマガジン (2004), No. 13. In Japanese.