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    • BioMagResBank (BMRB) as a Resource for Structural Biology
    • Pedro R. Romero, Naohiro Kobayashi, Jonathan R. Wedell, Kumaran Baskaran, Takeshi Iwata, Masashi Yokochi, Dimitri Maziuk, Hongyang Yao, Toshimichi Fujiwara, Genji Kurusu, Eldon L. Ulrich, Jeffrey C. Hoch, John L. Markley
    • Structural Bioinformatics. Methods in Molecular Biology
    • 2112
    • 187-218
    • 2020
  • Protein Data Bank: the single global archive for 3D macromolecular structure data
    wwPDB consortium
    Nucleic Acids Research 47(D1): D520-D528 (2019) [PubMed][doi:10.1093/nar/gky949]
  • New tools and functions in Data-out activities at Protein Data Bank Japan (PDBj)
    Kinjo, A.R., Bekker, G.-J., Wako, H., Endo, S., Tsuchiya, Y., Sato, H., Nishi, H., Kinoshita, K., Suzuki, H., Kawabata, T., Yokochi, M., Iwata, T., Kobayashi, N., Fujiwara, T., Kurisu, G. and Nakamura, H.
    Protein Science 27 (1): 95-102 (2018) [PubMed][doi:10.1002/pro.3273]
  • Protein Data Bank Japan (PDBj): Updated user interfaces, Resource Description Framework, analysis tools for large structures
    Kinjo, A.R., Bekker, G.-J., Suzuki, H., Tsuchiya, Y., Kawabata, T., Ikegawa, Y., Nakamura, H.
    Nucleic Acids Research 45(D1): D282-D288 (2017) [doi:10.1093/nar/gkw962]
  • Molmil: a molecular viewer for the PDB and beyond
    Bekker, G.-J., Nakamura, H., Kinjo, A.R.
    Journal of Cheminformatics 8:42 (2016) [doi:10.1186/s13321-016-0155-1]
  • Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB
    Suzuki, H., Kawabata, T., Nakamura, H.
    Bioinformatics 32 (4): 619-620 (2016) [PubMed][doi:10.1093/bioinformatics/btv614]
  • A novel loss-of-function mutation of GATA3 (p.R299Q) in a Japanese family with Hypoparathyroidism, Deafness, and Renal Dysplasia (HDR) syndrome
    Okawa, T., Yoshida, M., Usui, T., Kudou, T., Iwasaki, Y., Fukuoka, K., Takahashi, N., Uehara, Y., Oiso, Y.
    BMC Endocrine Disorders 15: 66 (2015) [doi:10.1186/s12902-015-0065-7]
  • The Protein Data Bank archive as an open data resource
    Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.
    Journal of Computer-Aided Molecular Design 28 (10): 1009-1014 (2014) [doi:10.1007/s10822-014-9770-y]
  • How Community Has Shaped the Protein Data Bank
    Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.
    Structure 21 (9): 1485-1491 (2013) [doi:10.1016/j.str.2013.07.010]
  • Exhaustive comparison and classification of ligand-binding surfaces in proteins.
    Murakami, Y., Kinoshita, K., Kinjo, A.R., Nakamura, H.
    Protein Science 22 (10): 1379-1391 (2013) [PubMed][doi:10.1002/pro.2329]
  • Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables.
    Wako, H., Endo, S.
    Comp.Biol.Chem. 44 22-30 (2013) [PubMed][doi:10.1016/j.compbiolchem.2013.02.006]
  • Functional structural motifs for protein-ligand, protein-protein and protein-nucleic acid interactions and their connection to supersecondary structures.
    Kinjo, A.R., Nakamura, H.
    Methods in Molecular Biology 932: 295-315 (2013) [PubMed][doi:10.1007/978-1-62703-065-6_18]
  • The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future
    Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.
    Structure 20 (3): 391-396 (2012) [PubMed][doi:10.1016/j.str.2012.01.010]
  • The future of the protein data bank.
    Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.
    Biopolymers 99 (2): (2012) [PubMed][doi:10.1002/bip.22132]
  • GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.
    Kinjo, A.R., Nakamura, H.
    BIOPHYSICS 8: 79-94 (2012) [doi:10.2142/biophysics.8.79]
  • Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.
    Kinjo, A.R., Suzuki, H., Yamashita, R., Ikegawa, Y., Kudou, T., Igarashi, R., Kengaku, Y., Cho, H., Standley, D.M., Nakagawa, A., Nakamura, H.
    Nucleic Acids Research 40(D1): D453-D460 (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, D.M., Yamashita, R., Kinjo, A.R., Toh, H., Nakamura, H.
    Bioinformatics 26: 1258-1259(2010) [PubMed][doi:10.1093/bioinformatics/btq116]
  • 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]
  • 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)]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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.
  • 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]
  • 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]
  • 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]
Created: 2012-04-13 (last edited: 4 months ago)2020-07-03
PDB entries from 2020-10-28