Organizations:

• 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 Wiley & Sons 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:

• 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]
• 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]