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Volumn 1607, Issue , 2017, Pages 627-641

Protein Data Bank (PDB): The single global macromolecular structure archive

Author keywords

3D electron microscopy; Chemical Component Dictionary; Crystallography; Integrative or hybrid methods; NEF; NMR Exchange Format; NMR spectroscopy; NMR STAR; PDB; PDBx mmCIF; Protein Data Bank; Worldwide Protein Data Bank; wwPDB

Indexed keywords

CHEMICAL STRUCTURE; MACROMOLECULE; METADATA; PROTEIN DATA BANK; STANDARDIZATION; CHEMISTRY; ELECTRON MICROSCOPY; HUMAN; INTERNATIONAL COOPERATION; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; STEREOISOMERISM; ULTRASTRUCTURE; UTILIZATION; X RAY CRYSTALLOGRAPHY;

EID: 85020222480     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-7000-1_26     Document Type: Chapter
Times cited : (703)

References (56)
  • 1
    • 0345383833 scopus 로고
    • Protein Data Bank
    • Protein Data Bank
    • Protein Data Bank (1971) Protein Data Bank. Nature New Biology 233:223
    • (1971) Nature New Biology , vol.233 , pp. 223
  • 2
    • 0001266102 scopus 로고
    • A three-dimensional model of the myoglobin molecule obtained by X-ray analysis
    • Kendrew JC, Bodo G, Dintzis HM et al (1958) A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181:662-666
    • (1958) Nature , vol.181 , pp. 662-666
    • Kendrew, J.C.1    Bodo, G.2    Dintzis, H.M.3
  • 3
    • 36949091243 scopus 로고
    • Structure of myoglobin: A three-dimensional Fourier synthesis at 2 Å resolution
    • Kendrew JC, Dickerson RE, Strandberg BE et al (1960) Structure of myoglobin: a three-dimensional Fourier synthesis at 2 Å resolution. Nature 185:422-427
    • (1960) Nature , vol.185 , pp. 422-427
    • Kendrew, J.C.1    Dickerson, R.E.2    Strandberg, B.E.3
  • 4
    • 0014936345 scopus 로고
    • Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Ångstrom units resolution
    • Bolton W, Perutz MF (1970) Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Ångstrom units resolution. Nature 228:551-552
    • (1970) Nature , vol.228 , pp. 551-552
    • Bolton, W.1    Perutz, M.F.2
  • 5
    • 36949066642 scopus 로고
    • Structure of haemoglobin: A three-dimensional Fourier synthesis at 5.5 Å resolution, obtained by X-ray analysis
    • Perutz MF, Rossmann MG, Cullis AF et al (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5 Å resolution, obtained by X-ray analysis. Nature 185:416-422
    • (1960) Nature , vol.185 , pp. 416-422
    • Perutz, M.F.1    Rossmann, M.G.2    Cullis, A.F.3
  • 6
    • 0007586570 scopus 로고
    • Cold Spring Laboratory, Cold Spring Laboratory Press, Cold Spring Harbor, NY
    • Cold Spring Laboratory (1972) Cold Spring Harbor Symposia on quantitative biology, vol 36. Cold Spring Laboratory Press, Cold Spring Harbor, NY
    • (1972) Cold Spring Harbor Symposia on Quantitative Biology , vol.36
  • 7
    • 37549024654 scopus 로고    scopus 로고
    • The Protein Data Bank: A historical perspective
    • Berman H (2008) The Protein Data Bank: a historical perspective. Acta Crystallogr A 64:88-95
    • (2008) Acta Crystallogr A , vol.64 , pp. 88-95
    • Berman, H.1
  • 8
    • 0031182215 scopus 로고    scopus 로고
    • The first years of the Protein Data Bank
    • Meyer EF (1997) The first years of the Protein Data Bank. Protein Sci 6:1591-1597
    • (1997) Protein Sci , vol.6 , pp. 1591-1597
    • Meyer, E.F.1
  • 9
    • 14844301239 scopus 로고
    • Policy on publication and the deposition of data from crystallographic studies of biological macromolecules
    • International Union of Crystallography
    • International Union of Crystallography (1989) Policy on publication and the deposition of data from crystallographic studies of biological macromolecules. Acta Crystallogr A 45:658
    • (1989) Acta Crystallogr A , vol.45 , pp. 658
  • 10
    • 0032214622 scopus 로고    scopus 로고
    • Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules
    • Sussman JL, Lin D, Jiang J et al (1998) Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr D Biol Crystallogr 54:1078-1084
    • (1998) Acta Crystallogr D Biol Crystallogr , vol.54 , pp. 1078-1084
    • Sussman, J.L.1    Lin, D.2    Jiang, J.3
  • 12
    • 45949088702 scopus 로고    scopus 로고
    • Protein structure databases with new web services for structural biology and biomedical research
    • Standley DM, Kinjo AR, Kinoshita K et al (2008) Protein structure databases with new web services for structural biology and biomedical research. Brief Bioinform 9:276-285
    • (2008) Brief Bioinform , vol.9 , pp. 276-285
    • Standley, D.M.1    Kinjo, A.R.2    Kinoshita, K.3
  • 14
    • 84976877697 scopus 로고    scopus 로고
    • PDBe: Improved accessibility of macromolecular structure data from PDB and EMDB
    • Velankar S, van Ginkel G, Alhroub Y et al (2016) PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res 44:D385-D395
    • (2016) Nucleic Acids Res , vol.44 , pp. D385-D395
    • Velankar, S.1    Van Ginkel, G.2    Alhroub, Y.3
  • 16
    • 0024572653 scopus 로고
    • Creation of a nuclear magnetic resonance data repository and literature database
    • Ulrich EL, Markley JL, Kyogoku Y (1989) Creation of a nuclear magnetic resonance data repository and literature database. Protein Seq Data Anal 2:23-37
    • (1989) Protein Seq Data Anal , vol.2 , pp. 23-37
    • Ulrich, E.L.1    Markley, J.L.2    Kyogoku, Y.3
  • 17
    • 41149116500 scopus 로고    scopus 로고
    • BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): New policies affecting biomolecular NMR depositions
    • Markley JL, Ulrich EL, Berman HM et al (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40:153-155
    • (2008) J Biomol NMR , vol.40 , pp. 153-155
    • Markley, J.L.1    Ulrich, E.L.2    Berman, H.M.3
  • 19
    • 75549089584 scopus 로고    scopus 로고
    • PDBe: Protein Data Bank in Europe
    • Velankar S, Best C, Beuth B et al (2010) PDBe: Protein Data Bank in Europe. Nucleic Acids Res 38:D308-D317
    • (2010) Nucleic Acids Res , vol.38 , pp. D308-D317
    • Velankar, S.1    Best, C.2    Beuth, B.3
  • 20
    • 0033924043 scopus 로고    scopus 로고
    • AutoDep: A web-based system for deposition and validation of macromolecular structural information
    • Lin D, Manning NO, Jiang J et al (2000) AutoDep: a web-based system for deposition and validation of macromolecular structural information. Acta Crystallogr D Biol Crystallogr 56:828-841
    • (2000) Acta Crystallogr D Biol Crystallogr , vol.56 , pp. 828-841
    • Lin, D.1    Manning, N.O.2    Jiang, J.3
  • 21
    • 33644873707 scopus 로고    scopus 로고
    • E-MSD: Improving data deposition and structure quality
    • Tagari M, Tate J, Swaminathan GJ et al (2006) E-MSD: improving data deposition and structure quality. Nucleic Acids Res 34:D287-D290
    • (2006) Nucleic Acids Res , vol.34 , pp. D287-D290
    • Tagari, M.1    Tate, J.2    Swaminathan, G.J.3
  • 22
    • 80054078285 scopus 로고    scopus 로고
    • A new generation of crystallographic validation tools for the Protein Data Bank
    • Read RJ, Adams PD, Arendall WB et al (2011) A new generation of crystallographic validation tools for the Protein Data Bank. Structure 19:1395-1412
    • (2011) Structure , vol.19 , pp. 1395-1412
    • Read, R.J.1    Adams, P.D.2    Arendall, W.B.3
  • 23
    • 84883476906 scopus 로고    scopus 로고
    • Recommendations of the wwPDB NMR Validation Task Force
    • Montelione GT, Nilges M, Bax A et al (2013) Recommendations of the wwPDB NMR Validation Task Force. Structure 21:1563-1570
    • (2013) Structure , vol.21 , pp. 1563-1570
    • Montelione, G.T.1    Nilges, M.2    Bax, A.3
  • 24
    • 84863011711 scopus 로고    scopus 로고
    • Outcome of the first electron microscopy validation task force meeting
    • Henderson R, Sali A, Baker ML et al (2012) Outcome of the first electron microscopy validation task force meeting. Structure 20:205-214
    • (2012) Structure , vol.20 , pp. 205-214
    • Henderson, R.1    Sali, A.2    Baker, M.L.3
  • 25
    • 33746949838 scopus 로고    scopus 로고
    • Outcome of a workshop on archiving structural models of biological macromolecules
    • Berman HM, Burley SK, Chiu W et al (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14:1211-1217
    • (2006) Structure , vol.14 , pp. 1211-1217
    • Berman, H.M.1    Burley, S.K.2    Chiu, W.3
  • 27
    • 84878835514 scopus 로고    scopus 로고
    • Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB
    • Trewhella J, Hendrickson WA, Kleywegt GJ et al (2013) Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure 21:875-881
    • (2013) Structure , vol.21 , pp. 875-881
    • Trewhella, J.1    Hendrickson, W.A.2    Kleywegt, G.J.3
  • 28
    • 84941069273 scopus 로고    scopus 로고
    • SASBDB, a repository for biological small-angle scattering data
    • Valentini E, Kikhney AG, Previtali G et al (2015) SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res 43:D357-D363
    • (2015) Nucleic Acids Res , vol.43 , pp. D357-D363
    • Valentini, E.1    Kikhney, A.G.2    Previtali, G.3
  • 30
    • 84964824712 scopus 로고    scopus 로고
    • Outcome of the First wwPDB/CCDC/ D3R Ligand Validation Workshop.
    • Adams PD, Aertgeerts K, Bauer C et al (2016) Outcome of the First wwPDB/CCDC/ D3R Ligand Validation Workshop. Structure 24:502-50831.
    • (2016) Structure , vol.24 , pp. 502-50831
    • Adams, P.D.1    Aertgeerts, K.2    Bauer, C.3
  • 31
    • 84960381776 scopus 로고    scopus 로고
    • Data publication with the structural biology data grid supports live analysis
    • Meyer PA, Socias S, Key J et al (2016) Data publication with the structural biology data grid supports live analysis. Nature Commun 7:10882
    • (2016) Nature Commun , vol.7 , pp. 10882
    • Meyer, P.A.1    Socias, S.2    Key, J.3
  • 32
    • 0037263885 scopus 로고    scopus 로고
    • Macromolecular structure determination by NMR spectroscopy
    • In: Bourne PE, Weissig H (eds) , John Wiley & Sons, Inc., Hoboken, NJ
    • Markley JL, Ulrich EL, Westler WM et al (2003) Macromolecular structure determination by NMR spectroscopy. In: Bourne PE, Weissig H (eds) Structural bioinformatics. John Wiley & Sons, Inc., Hoboken, NJ, pp 89-113
    • (2003) Structural Bioinformatics. , pp. 89-113
    • Markley, J.L.1    Ulrich, E.L.2    Westler, W.M.3
  • 34
    • 84961393393 scopus 로고    scopus 로고
    • EMPIAR: A public archive for raw electron microscopy image data
    • Iudin A, Korir PK, Salavert-Torres J et al (2016) EMPIAR: a public archive for raw electron microscopy image data. Nat Methods 13:387
    • (2016) Nat Methods , vol.13 , pp. 387
    • Iudin, A.1    Korir, P.K.2    Salavert-Torres, J.3
  • 35
    • 0017411710 scopus 로고
    • Protein Data Bank: A computer-based archival file for macromolecular structures
    • Bernstein FC, Koetzle TF, Williams GJB et al (1977) Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535-542
    • (1977) J Mol Biol , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.3
  • 38
    • 16344364140 scopus 로고    scopus 로고
    • PDBML: The representation of archival macromolecular structure data in XML
    • Westbrook J, Ito N, Nakamura H et al (2005) PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21:988-992
    • (2005) Bioinformatics , vol.21 , pp. 988-992
    • Westbrook, J.1    Ito, N.2    Nakamura, H.3
  • 39
    • 84862238809 scopus 로고    scopus 로고
    • Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format
    • Kinjo AR, Suzuki H, Yamashita R et al (2012) Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res 40:D453-D460
    • (2012) Nucleic Acids Res , vol.40 , pp. D453-D460
    • Kinjo, A.R.1    Suzuki, H.2    Yamashita, R.3
  • 40
    • 84965005779 scopus 로고    scopus 로고
    • Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
    • Yokochi M, Kobayashi N, Ulrich EL et al (2016) Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J Biomed Semantics 7:16
    • (2016) J Biomed Semantics , vol.7 , pp. 16
    • Yokochi, M.1    Kobayashi, N.2    Ulrich, E.L.3
  • 41
    • 0034512176 scopus 로고    scopus 로고
    • SasCIF: An extension of core Crystallographic Information File for SAS
    • Malfois M, Svergun DI (2000) sasCIF: an extension of core Crystallographic Information File for SAS. J Appl Crystallogr 33:812-816
    • (2000) J Appl Crystallogr , vol.33 , pp. 812-816
    • Malfois, M.1    Svergun, D.I.2
  • 42
    • 0345785707 scopus 로고    scopus 로고
    • STAR/CIF macromolecular NMR data dictionaries and data file formats
    • Ulrich EL, Argentar D, Klimowicz A et al (1996) STAR/CIF macromolecular NMR data dictionaries and data file formats. Acta Crystallogr A 52:C577-C577
    • (1996) Acta Crystallogr A , vol.52 , pp. C577-C577
    • Ulrich, E.L.1    Argentar, D.2    Klimowicz, A.3
  • 43
    • 77957730491 scopus 로고    scopus 로고
    • The Worldwide Protein Data Bank
    • In: Gu J, Bourne PE, 2nd edn. Wiley, Hoboken, NJ
    • Berman HM, Henrick K, Nakamura H et al (2009) The Worldwide Protein Data Bank. In: Gu J, Bourne PE (eds) Structural bioinformatics, 2nd edn. Wiley, Hoboken, NJ, pp 293-303
    • (2009) Structural Bioinformatics , pp. 293-303
    • Berman, H.M.1    Henrick, K.2    Nakamura, H.3
  • 44
    • 84862158668 scopus 로고    scopus 로고
    • NRG-CING: Integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
    • Doreleijers JF, Vranken WF, Schulte C et al (2012) NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res 40:D519-D524
    • (2012) Nucleic Acids Res , vol.40 , pp. D519-D524
    • Doreleijers, J.F.1    Vranken, W.F.2    Schulte, C.3
  • 45
    • 71049172008 scopus 로고    scopus 로고
    • The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries
    • Doreleijers JF, Vranken WF, Schulte C et al (2009) The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. J Biomol NMR 45:389-396
    • (2009) J Biomol NMR , vol.45 , pp. 389-396
    • Doreleijers, J.F.1    Vranken, W.F.2    Schulte, C.3
  • 46
    • 84930386838 scopus 로고    scopus 로고
    • NMR Exchange Format: A unified and open standard for representation of NMR restraint data
    • Gutmanas A, Adams PD, Bardiaux B et al (2015) NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol 22:433-434
    • (2015) Nat Struct Mol Biol , vol.22 , pp. 433-434
    • Gutmanas, A.1    Adams, P.D.2    Bardiaux, B.3
  • 47
    • 84927774990 scopus 로고    scopus 로고
    • The chemical component dictionary: Complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
    • Westbrook JD, Shao C, Feng Z et al (2015) The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. Bioinformatics 31:1274-1278
    • (2015) Bioinformatics , vol.31 , pp. 1274-1278
    • Westbrook, J.D.1    Shao, C.2    Feng, Z.3
  • 48
    • 84892723816 scopus 로고    scopus 로고
    • Improving the representation of peptidelike inhibitor and antibiotic molecules in the Protein Data Bank
    • Dutta S, Dimitropoulos D, Feng Z et al (2014) Improving the representation of peptidelike inhibitor and antibiotic molecules in the Protein Data Bank. Biopolymers 101:659-668
    • (2014) Biopolymers , vol.101 , pp. 659-668
    • Dutta, S.1    Dimitropoulos, D.2    Feng, Z.3
  • 49
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: A hub for protein information
    • UniProt Consortium
    • UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res 43:D204-D212
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-D212
  • 50
    • 38549094609 scopus 로고    scopus 로고
    • NORINE: A database of nonribosomal peptides
    • Caboche S, Pupin M, Leclere V et al (2008) NORINE: a database of nonribosomal peptides. Nucleic Acids Res 36:D326-D331
    • (2008) Nucleic Acids Res , vol.36 , pp. D326-D331
    • Caboche, S.1    Pupin, M.2    Leclere, V.3
  • 51
    • 84883481556 scopus 로고    scopus 로고
    • The Protein Model Portal—a comprehensive resource for protein structure and model information
    • Haas J, Roth S, Arnold K et al (2013) The Protein Model Portal—a comprehensive resource for protein structure and model information. Database 2013:bat031
    • (2013) Database 2013:Bat031
    • Haas, J.1    Roth, S.2    Arnold, K.3
  • 52
    • 84979084493 scopus 로고    scopus 로고
    • Application of nuclear magnetic resonance and hybrid methods to structure determination of complex systems
    • Prischi F, Pastore A (2016) Application of nuclear magnetic resonance and hybrid methods to structure determination of complex systems. Adv Exper Med Biol 896:351-368
    • (2016) Adv Exper Med Biol , vol.896 , pp. 351-368
    • Prischi, F.1    Pastore, A.2
  • 53
    • 84950245428 scopus 로고    scopus 로고
    • Structural analysis of multi-helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA
    • Cornilescu G, Didychuk AL, Rodgers ML et al (2016) Structural analysis of multi-helical RNAs by NMR-SAXS/WAXS: application to the U4/U6 di-snRNA. J Mol Biol 428:777-789
    • (2016) J Mol Biol , vol.428 , pp. 777-789
    • Cornilescu, G.1    Didychuk, A.L.2    Rodgers, M.L.3
  • 54
    • 84974627334 scopus 로고    scopus 로고
    • Hybrid approaches to structural characterization of conformational ensembles of complex macromolecular systems combining NMR residual dipolar couplings and solution X-ray scattering
    • Venditti V, Egner TK, Clore GM (2016) Hybrid approaches to structural characterization of conformational ensembles of complex macromolecular systems combining NMR residual dipolar couplings and solution X-ray scattering. Chem Rev 116:6305-6322
    • (2016) Chem Rev , vol.116 , pp. 6305-6322
    • Venditti, V.1    Egner, T.K.2    Clore, G.M.3
  • 55
    • 84907323467 scopus 로고    scopus 로고
    • Molecular architecture of the 40SeIF1eIF3 translation initiation complex
    • Erzberger JP, Stengel F, Pellarin R et al (2014) Molecular architecture of the 40SeIF1eIF3 translation initiation complex. Cell 158:1123-1135
    • (2014) Cell , vol.158 , pp. 1123-1135
    • Erzberger, J.P.1    Stengel, F.2    Pellarin, R.3
  • 56
    • 84936847521 scopus 로고    scopus 로고
    • Outcome of the First wwPDB Hybrid/ Integrative Methods Task Force Workshop
    • Sali A, Berman HM, Schwede T et al (2015) Outcome of the First wwPDB Hybrid/ Integrative Methods Task Force Workshop. Structure 23:1156-1167
    • (2015) Structure , vol.23 , pp. 1156-1167
    • Sali, A.1    Berman, H.M.2    Schwede, T.3


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