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List of Publications

Organizations:

  • The future of the protein data bank.
    Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
    Biopolymers 99 (2): (2012) [PubMed] [doi:10.1002/bip.22132]
  • Outcome of a Workshop on Applications of Protein Models in Biomedical Research
    Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., Dunbrack Jr., R.L., Fidelis, K., Fiser, A., Godzik, A., Huang, Y.J., Humblet, C., Jacobson, M.P., Joachimiak, A., Krystek Jr., S.R., Kortemme, T., Kryshtafovych, A., Montelione, G.T., Moult, J., Murray, D., Sanchez, R., Sosnick, T.R., Standley, D.M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J.D., Wilson, I.A.
    Structure 17 (2): 151-159 (2009) [PubMed] [doi:10.1016/j.str.2008.12.014]
  • Data Deposition and Annotation at the Worldwide Protein Data Bank
    Dutta, S., Burkhardt, K., Young, J., Swaminathan, G.J., Matsuura, T., Henrick, K., Nakamura, H., Berman, H.M.
    Mol. Biotechnol. 42 (1): 1-13 (2009) [PubMed] [doi:10.1007/s12033-008-9127-7]
  • BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions
    Markley, J.L., Ulrich, E.L., Berman, H.M., Henrick, K., Nakamura, H., Akutsu, H.
    J. Biomol. NMR 40 (3): 153-155 (2008) [PubMed] [doi:10.1007/s10858-008-9221-y]
  • Remediation of the protein data bank archive
    Henrick, K., Feng, Z., Bluhm, W.F., Dimitropoulos, D., Doreleijers, J.F., Dutta, S., Flippen-Anderson, J.L., Ionides, J., Kamada, C., Krissinel, E., Lawson, C.L., Markley, J.L., Nakamura, H., Newman, R., Shimizu, Y., Swaminathan, J., Velankar, S., Ory, J., E. Ulrich, E.L., Vranken, W., Westbrook, J.D., Yamashita, R., Yang, H., Young, J., Yousufuddin, M., Berman, H.M.
    Nucleic Acids Res. 36 (Database issue): D426-D433 (2008) [PubMed] [doi:10.1093/nar/gkm937]
  • BioMagResBank
    Ulrich,E.L., Akutsu H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C.F., Tolmie, D.E., Kent Wenger, R., Yao, H., Markley, J.L.
    Nucleic Acids Res. 36 (Database issue): D402-408 (2008) [doi:10.1093/nar/gkm957]
  • Realism about PDB
    Berman, H.M., Henrick, K., Nakamura, H., Markley, J.L., Bourne, P.E., Westbrook, J.D.
    Nature Biotechnology 25: 845-846 (2007) [PubMed] [doi:10.1038/nbt0807-845]
  • Reply to: Building meaningful models of glycoproteins
    Berman, H.M., Henrick, K., Nakamura, H., Markley, J.L.
    Nature Structure Molecular Biology 14: 354-355 (2007) [doi:10.1038/nsmb0507-354b]
  • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
    Berman, H.M. , Henrick, K., Nakamura, H., Markley, J.L.
    Nucleic Acids Research 35 (Database issue): D301-D303 (2007) [PubMed] [doi:10.1093/nar/gkl971]
  • Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules
    Berman, H.M., Burley, S.K., Chiu, W., Sail, A., Adzhubei, A., Bourne, P.E., Bryant, S.H., Dunbrack Jr., R.L., Fidelis, K., Frabk, J., Godzik, A., Henrick, K., Joachimiak, A., Heymann, B., Jones, D., Markley, J.L., Moult, J., Montelione, G.T., Orengo, C., Rossmann, M.G., Rost, B., Saibil, H., Schwede, T., Standley, D.M., Westbrook, J.D.
    Structure 14 (8): 1211-1217 (2006) [PubMed] [doi:10.1016/j.str.2006.06.005]
  • The Protein Data Bank (PDB) and the World Wide PDB
    Berman, H.M., Nakamura, H., Henrick, K.
    In: Jorde L.B., Little P.F.R., Dunn M.J., Subramaniam S., editors. Encyclopedia of Genomics, Proteomics, and Bioinformatics. 7: John WileySons Ltd, Chichester; 2005. pp.3335-3339.
  • Announcing the world wide Protein Data Bank
    Berman, H.M., Henrick, K., Nakamura, H.
    Nature Structural Biology 10 (12): 980 (2003) [PubMed] [doi:10.1038/nsb1203-980]

Research and Tools for PDBj:

  • Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.
    Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H.
    Nucleic Acids Research 40(D1) : (2012) [PubMed] [doi:10.1093/nar/gkr811]
  • A comparative study of conservation and variation scores
    Johansson, F., Toh, H.
    BMC Bioinformatics 11 : (2010) [PubMed] [doi:10.1186/1471-2105-11-388]
  • Relative von neumann entropy for evaluating amino Acid conservation
    Johansson, F., Toh, H.
    J Bioinform Comput Biol 8 (5): 809-823 (2010) [PubMed] [doi:10.1142/S021972001000494X]
  • PDBj Mine: Design and implementation of relational database interface for Protein Data Bank Japan
    Kinjo, A.R., Yamashita, R., Nakamura, H.
    Database 2010 : baq021 (2010) [PubMed] [doi:10.1093/database/BAQ021]
  • Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study
    Kinjo, A.R., 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]
  • Comprehensive structural classification of ligand-binding motifs in proteins
    Kinjo, A.R., Nakamura, H.
    Structure 17 (2): 234-246 (2009) [PubMed] [doi:10.1016/j.str.2008.11.009]
  • Structure-based functional annotation of protein sequences guided by comparative models
    Standley, D.M., Kinjo, A.R., Lis, M., van der Giezen, M., Nakamura, H.
    Proceedings of the Second International Symposium on Optimization and Systems Biology (ed. Luonan Chen) Lijiang China. 395-403 (2008) [pdf (at APORC website)]
  • Protein multiple sequence alignment
    Do, C.B., Katoh, K.
    Methods in Molecular Biology 484: 379-413 (2008) [PubMed] [doi:10.1007/978-1-59745-398-1_25]
  • Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
    Katoh K., Toh H.
    BMC Bioinformatics 9: 212-224 (2008) [PubMed] [doi:10.1186/1471-2105-9-212]
  • Recent developments in the MAFFT multiple sequence alignment program
    Katoh, K., Toh, H.
    Brief. Bioinform. 9 (4): 286-298 (2008) [PubMed] [doi:10.1093/bib/bbn013]
  • Protein structure databases with new web services for structural biology and biomedical research
    Standley, D.M., Kinjo, A.R., Kinoshita, K., Nakamura, H.
    Briefings in Bioinformatics 9 (4): 276-285 (2008) [PubMed] [doi:10.1093/bib/bbn015]
  • Functional annotation by sequence-weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan
    Standley, D.M., Toh, H., Nakamura, H.
    PROTEINS 72 (4): 1333-1351 (2008) [PubMed] [doi:10.1002/prot.22015]
  • Similarity search for local protein structures at atomic resolution by exploiting a database management system
    Kinjo, A.R., Nakamura, H.
    BIOPHYSICS 3: 75-84 (2007) [doi:10.2142/biophysics.3.75]
  • eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    Kinoshita, K., Murakami, Y., Nakamura, H.
    Nucleic Acids Res. 35: W398-402 (2007) [PubMed] [doi:10.1093/nar/gkm351]
  • ASH structure alignment package: sensitivity and selectivity in domain classification
    Standley, D.M., Toh, H., Nakamura, H.
    BMC Bioinformatics 8: 116-123 (2007) [PubMed] [doi:10.1186/1471-2105-8-116]
  • GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures
    Standley, D.M., Toh, H., Nakamura, H.
    BMC Bioinformatics 6: 221-239 (2005) [PubMed] [doi:10.1186/1471-2105-6-221]
  • PDBML: The representation of archival macromolecular structure data in XML
    Westbrook, J.D., Ito, N., Nakamura, H., Henrick, K., Berman, H.M.
    Bioinformatics 21 (7): 988-992 (2005) [PubMed] [doi:10.1093/bioinformatics/bti082]
  • Identification of the ligand binding sites on the molecular surface of proteins
    Kinoshita, K., Nakamura, H.
    Protein Science 14 (3): 711-718 (2005) [PubMed] [doi:10.1110/ps.041080105]
  • ProMode: a database of normal mode analyses on protein molecules with a full-atom model
    Wako, H., Kato, M., Endo, S.
    Bioinformatics 20 (13):2035-2043 (2004) [PubMed] [doi:10.1093/bioinformatics/bth197]
  • eF-site and PDBjViewer: database and viewer for protein functional sites
    Kinoshita, K., Nakamura, H.
    Bioinformatics 20 (8):1329-1330 (2004) [PubMed] [doi:10.1093/bioinformatics/bth073]
  • Detecting local structural similarity in proteins by maximizing number of equivalent residues
    Standley, D.M., Toh, H., Nakamura, H.
    Proteins 57 (2): 381-391 (2004) [PubMed] [doi:10.1002/prot.20211]
  • Protein informatics towards function identification
    Kinoshita, K., Nakamura, H.
    Current Opinion in Structural Biology 13 (3): 396-400 (2003) [PubMed] [doi:10.1016/S0959-440X(03)00074-5]
  • Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
    Kinoshita, K., Nakamura, H.
    Protein Science 12 (8): 1589-1595 (2003) [PubMed] [doi:10.1110/ps.0368703]
  • Identification of protein functions from a molecular surface database, eF-site
    Kinoshita, K., Furui, J., Nakamura, H.
    J. Struct. Funct. Genomics 2 (1): 9-22 (2001) [PubMed] [doi:10.1023/A:1011318527094]