메뉴 건너뛰기




Volumn 40, Issue D1, 2012, Pages

Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; DATA PROCESSING; INFORMATION CENTER; INFORMATION RETRIEVAL; JAPAN; MACROMOLECULE; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK JAPAN; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN STRUCTURE; STANDARDIZATION; WEB BROWSER;

EID: 84862238809     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr811     Document Type: Article
Times cited : (122)

References (40)
  • 1
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • DOI 10.1093/nar/gkl971
    • Berman,H., Henrick,K., Nakamura,H. and Markley,J.L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303. (Pubitemid 46056219)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 2
    • 45949088702 scopus 로고    scopus 로고
    • Protein structure databases with new web services for structural biology and biomedical research
    • DOI 10.1093/bib/bbn015, Special Issue: Critical Technologies for Bioinformatics
    • Standley,D.M., Kinjo,A.R., Kinoshita,K. and Nakamura,H. (2008) Protein structure databases with new web services for structural biology and biomedical research. Brief. Bioinformatics, 9, 276-285. (Pubitemid 351890824)
    • (2008) Briefings in Bioinformatics , vol.9 , Issue.4 , pp. 276-285
    • Standley, D.M.1    Kinjo, A.R.2    Kinoshita, K.3    Nakamura, H.4
  • 6
    • 16344364140 scopus 로고    scopus 로고
    • PDBML: The representation of archival macromolecular structure data in XML
    • DOI 10.1093/bioinformatics/bti082
    • Westbrook,J., Ito,N., Nakamura,H., Henrick,K. and Berman,H.M. (2005) PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics, 21, 988-992. (Pubitemid 40467920)
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 988-992
    • Westbrook, J.1    Ito, N.2    Nakamura, H.3    Henrick, K.4    Berman, H.M.5
  • 11
    • 33748847737 scopus 로고    scopus 로고
    • The Life Sciences Semantic Web is full of creeps!
    • DOI 10.1093/bib/bbl025
    • Good,B.M. and Wilkinson,M.D. (2006) The life sciences semantic web is full of creeps! Brief. Bioinform., 7, 275-286. (Pubitemid 44417949)
    • (2006) Briefings in Bioinformatics , vol.7 , Issue.3 , pp. 275-286
    • Good, B.M.1    Wilkinson, M.D.2
  • 12
    • 41149160103 scopus 로고    scopus 로고
    • Biological data integration using Semantic Web technologies
    • Pasquier,C. (2008) Biological data integration using Semantic Web technologies. Biochimie, 584, 584-594.
    • (2008) Biochimie , vol.584 , pp. 584-594
    • Pasquier, C.1
  • 14
    • 5444246382 scopus 로고    scopus 로고
    • 27 September 2011, date last accessed
    • Manola,F. and Miller,E. (eds) (2004) RDF Primer, World Wide Web Consortium. http://www.w3.org/TR/rdf-primer (27 September 2011, date last accessed).
    • (2004) RDF Primer
    • Manola, F.1    Miller, E.2
  • 17
    • 0034020917 scopus 로고    scopus 로고
    • STAR/mmCIF: An ontology for macromolecular structure
    • Westbrook,J.D. and Bourne,P.E. (2000) STAR/mmCIF: an ontology for macromolecular structure. Bioinformatics, 159, 159-168. (Pubitemid 30248593)
    • (2000) Bioinformatics , vol.16 , Issue.2 , pp. 159-168
    • Westbrook, J.D.1    Bourne, P.E.2
  • 18
    • 0003508228 scopus 로고    scopus 로고
    • 27 September 2011, date last accessed
    • Fallside,D.C. and Walmsley,P. (eds) (2004) XML Schema Part 0: Primer, World Wide Web Consortium. http://www.w3.org/TR/xmlschema-0/ (27 September 2011, date last accessed).
    • (2004) XML Schema Part 0: Primer
    • Fallside, D.C.1    Walmsley, P.2
  • 19
    • 0003420124 scopus 로고    scopus 로고
    • Version 1.0 27 September 2011, date last accessed
    • Clark,J. (ed.) (1999) XSL Transformations (XSLT) Version 1.0, World Wide Web Consortium. http://www.w3.org/TR/xslt/(27 September 2011, date last accessed).
    • (1999) XSL Transformations (XSLT)
    • Clark, J.1
  • 23
    • 34248201703 scopus 로고    scopus 로고
    • ASH structure alignment package: Sensitivity and selectivity in domain classification
    • Standley,D.M., Toh,H. and Nakamura,H. (2007) ASH structure alignment package: sensitivity and selectivity in domain classification. BMC Bioinformatics, 8, 116.
    • (2007) BMC Bioinformatics , vol.8 , pp. 116
    • Standley, D.M.1    Toh, H.2    Nakamura, H.3
  • 24
    • 77952792362 scopus 로고    scopus 로고
    • SeSAW: Balancing sequence and structural information in protein functional mapping
    • Standley,D.M., Yamashita,R., Kinjo,A.R., Toh,H. and Nakamura,H. (2010) SeSAW: balancing sequence and structural information in protein functional mapping. Bioinformatics, 26, 1258-1259.
    • (2010) Bioinformatics , vol.26 , pp. 1258-1259
    • Standley, D.M.1    Yamashita, R.2    Kinjo, A.R.3    Toh, H.4    Nakamura, H.5
  • 25
    • 38149096341 scopus 로고    scopus 로고
    • Similarity search for local protein structures at atomic resolution by exploiting a database management system
    • Kinjo,A.R. and Nakamura,H. (2007) Similarity search for local protein structures at atomic resolution by exploiting a database management system. Biophysics, 3, 75-84.
    • (2007) Biophysics , vol.3 , pp. 75-84
    • Kinjo, A.R.1    Nakamura, H.2
  • 26
    • 59649095965 scopus 로고    scopus 로고
    • Comprehensive structural classification of ligand binding motifs in proteins
    • Kinjo,A.R. and Nakamura,H. (2009) Comprehensive structural classification of ligand binding motifs in proteins. Structure, 17, 234-246.
    • (2009) Structure , vol.17 , pp. 234-246
    • Kinjo, A.R.1    Nakamura, H.2
  • 27
    • 77954759220 scopus 로고    scopus 로고
    • Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study
    • Kinjo,A.R. and Nakamura,H. (2010) Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. J. Mol. Biol., 399, 526-540.
    • (2010) J. Mol. Biol. , vol.399 , pp. 526-540
    • Kinjo, A.R.1    Nakamura, H.2
  • 28
    • 3042683893 scopus 로고    scopus 로고
    • eF-site and PDBjViewer: Database and viewer for protein functional sites
    • DOI 10.1093/bioinformatics/bth073
    • Kinoshita,K. and Nakamura,H. (2004) eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics, 20, 1329-1330. (Pubitemid 38807590)
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1329-1330
    • Kinoshita, K.1    Nakamura, H.2
  • 29
    • 25444447367 scopus 로고    scopus 로고
    • GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures
    • Standley,D.M., Toh,H. and Nakamura,H. (2005) GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures. BMC Bioinformatics, 6, 221.
    • (2005) BMC Bioinformatics , vol.6 , pp. 221
    • Standley, D.M.1    Toh, H.2    Nakamura, H.3
  • 30
    • 4544295055 scopus 로고    scopus 로고
    • Detecting local structural similarity in proteins by maximizing number of equivalent residues
    • DOI 10.1002/prot.20211
    • Standley,D.M., Toh,H. and Nakamura,H. (2004) Detecting local structural similarity in proteins by maximizing number of equivalent residues. Proteins, 57, 381-391. (Pubitemid 39223743)
    • (2004) Proteins: Structure, Function and Genetics , vol.57 , Issue.2 , pp. 381-391
    • Standley, D.M.1    Toh, H.2    Nakamura, H.3
  • 31
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • DOI 10.1093/bib/bbn013, Special Issue: Critical Technologies for Bioinformatics
    • Katoh,K. and Toh,H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform., 9, 286-298. (Pubitemid 351890825)
    • (2008) Briefings in Bioinformatics , vol.9 , Issue.4 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 32
    • 33744780638 scopus 로고    scopus 로고
    • Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks
    • Kinjo,A.R. and Nishikawa,K. (2005) Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks. Biophysics, 1, 67-74.
    • (2005) Biophysics , vol.1 , pp. 67-74
    • Kinjo, A.R.1    Nishikawa, K.2
  • 33
    • 33749357045 scopus 로고    scopus 로고
    • CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
    • Kinjo,A.R. and Nishikawa,K. (2006) CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. BMC Bioinformatics, 7, 401.
    • (2006) BMC Bioinformatics , vol.7 , pp. 401
    • Kinjo, A.R.1    Nishikawa, K.2
  • 35
    • 0041842509 scopus 로고    scopus 로고
    • Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
    • DOI 10.1110/ps.0368703
    • Kinoshita,K. and Nakamura,H. (2003) Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci., 12, 1589-1595. (Pubitemid 36910039)
    • (2003) Protein Science , vol.12 , Issue.8 , pp. 1589-1595
    • Kinoshita, K.1    Nakamura, H.2
  • 36
    • 34547587452 scopus 로고    scopus 로고
    • EF-seek: Prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    • Kinoshita,K., Murakami,Y. and Nakamura,H. (2007) eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res., 35, W398-W402.
    • (2007) Nucleic Acids Res. , vol.35
    • Kinoshita, K.1    Murakami, Y.2    Nakamura, H.3
  • 37
    • 4544280144 scopus 로고    scopus 로고
    • ProMode: A database of normal mode analyses on protein molecules with a full-atom model
    • DOI 10.1093/bioinformatics/bth197
    • Wako,H., Kato,M. and Endo,S. (2004) ProMode: a database of normal mode analyses on protein molecules with a full-atom model. Bioinformatics, 20, 2035-2043. (Pubitemid 39236555)
    • (2004) Bioinformatics , vol.20 , Issue.13 , pp. 2035-2043
    • Wako, H.1    Kato, M.2    Endo, S.3
  • 39
    • 77957352833 scopus 로고    scopus 로고
    • Jmol a paradigm shift in crystallographic visualization
    • Hanson,R.M. (2010) Jmol a paradigm shift in crystallographic visualization. J. Appl. Crystallogr., 43, 1250-1260.
    • (2010) J. Appl. Crystallogr. , vol.43 , pp. 1250-1260
    • Hanson, R.M.1
  • 40
    • 77957996302 scopus 로고    scopus 로고
    • Direct visualization of secondary structures of F-actin by electron cryomicroscopy
    • Fujii,T., Iwane,A.H., Yanagida,T. and Namba,K. (2010) Direct visualization of secondary structures of F-actin by electron cryomicroscopy. Nature, 467, 724-728.
    • (2010) Nature , vol.467 , pp. 724-728
    • Fujii, T.1    Iwane, A.H.2    Yanagida, T.3    Namba, K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.