The archiving and dissemination of biological structure data

Current Opinion in Structural Biology

Volumn 40, Issue , 2016, Pages 17-22

  Berman, Helen M ^a   Burley, Stephen K ^a,b   Kleywegt, Gerard J ^c   Markley, John L ^d   Nakamura, Haruki ^e   Velankar, Sameer ^c  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

^e OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER PROGRAM; CRYSTALLOGRAPHY; DATA PROCESSING; INFORMATION CENTER; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN STRUCTURE; REVIEW; HUMAN; INFORMATION PROCESSING; PROCEDURES; PROTEIN DATABASE;

DATA CURATION; DATABASES, PROTEIN; HUMANS;

EID: 84979695950     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2016.06.018     Document Type: Review

References (44)

1. 1 Bernal, J.D., Crowfoot, D.M., X-ray photographs of crystalline pepsin. Nature 133 (1934), 794–795.
2. 2 Kendrew, J.C., Bodo, G., Dintzis, H.M., Parrish, R.G., Wyckoff, H., Phillips, D.C., A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181 (1958), 662–666.
3. 3 Kendrew, J.C., Dickerson, R.E., Strandberg, B.E., Hart, R.G., Davies, D.R., Phillips, D.C., Shore, V.C., Structure of myoglobin: a three-dimensional Fourier synthesis at 2 A resolution. Nature 185 (1960), 422–427.
4. 4 Perutz, M.F., Rossmann, M.G., Cullis, A.F., Muirhead, H., Will, G., North, A.C.T., Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5 Å resolution, obtained by X-ray analysis. Nature 185 (1960), 416–422.
5. 5 Bolton, W., Perutz, M.F., Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Ångstrom units resolution. Nature 228 (1970), 551–552.
6. 6• Cold Spring Harbor Symposia on Quantitative Biology, vol. 36, 1972, Cold Spring Laboratory Press This seminal meeting highlighted the key structures that had been determined and brought together the leading figures in structural biology. To quote David Phillips it was a ‘Coming of age.’.
7. 7 Protein Data Bank, Protein Data Bank. Nature New Biol., 233, 1971, 223.
8. 8 Meyer, E.F. Jr., Morimoto, C.N., Villarreal, J., Berman, H.M., Carrell, H.L., Stodola, R.K., Koetzle, T.F., Andrews, L.C., Bernstein, F.C., Bernstein, H.J., et al. CRYSNET, a crystallographic computing network with interactive graphics display. Fed Proc 33 (1974), 2402–2405.
9. 9 International Union of Crystallography, Policy on publication and the deposition of data from crystallographic studies of biological macromolecules. Acta Cryst, A45, 1989, 658.
10. 10•• Read, R.J., Adams, P.D., Arendall, W.B. 3rd, Brunger, A.T., Emsley, P., Joosten, R.P., Kleywegt, G.J., Krissinel, E.B., Lutteke, T., Otwinowski, Z., et al. A new generation of crystallographic validation tools for the protein data bank. Structure 19 (2011), 1395–1412 This paper contained a through analysis of methods that could be used for validation of structures determined by X-ray crystallography. The recommendations were used to create the validation tools used by the wwPDB.
11. 11•• Henderson, R., Sali, A., Baker, M.L., Carragher, B., Devkota, B., Downing, K.H., Egelman, E.H., Feng, Z., Frank, J., Grigorieff, N., et al. Outcome of the first electron microscopy validation task force meeting. Structure 20 (2012), 205–214 This paper was the first one to analyze what is needed to validate 3DEM maps and models. It is the basis for current research in this field.
12. 12•• Montelione, G.T., Nilges, M., Bax, A., Guntert, P., Herrmann, T., Richardson, J.S., Schwieters, C.D., Vranken, W.F., Vuister, G.W., Wishart, D.S., et al. Recommendations of the wwPDB NMR validation task force. Structure 21 (2013), 1563–1570 This paper made recommendations for how to validate structures determined by NMR, and is the basis for current ongoing research.
13. 13•• Adams, P.D., Aertgeerts, K., Bauer, C., Bell, J.A., Berman, H.M., Bhat, T.N., Blaney, J.M., Bolton, E., Bricogne, G., Brown, D., et al. Outcome of the first wwPDB/CCDC/D3R ligand validation workshop. Structure 24 (2016), 502–508 The criteria for judging the quality of ligands in protein complexes are laid out and will form the basis for improved validation of these molecules.
14. 14• Berman, H.M., Henrick, K., Nakamura, H., Announcing the worldwide Protein Data Bank. Nat Struct Biol, 10, 2003, 980 This is the formal announcement for how the Protein Data Bank will be managed by an international consortium.
15. 15 Brown, A., Bernal, J.D., The Sage of Science. 2005, Oxford University Press, Oxford.
16. 16• Lawson, C.L., Patwardhan, A., Baker, M.L., Hryc, C., Garcia, E.S., Hudson, B.P., Lagerstedt, I., Ludtke, S.J., Pintilie, G., Sala, R., et al. EMDataBank unified data resource for 3DEM. Nucleic Acids Res 44 (2016), D396–D403 This paper describes the procedures for streamlining the deposition and distribution of 3DEM maps and models.
17. 17 Iudin, A., Korir, P.K., Salavert-Torres, J., Kleywegt, G.J., Patwardhan, A., EMPIAR: a public archive for raw electron microscopy image data. Nat Methods, 2016, 13.
18. 18•• Berman, H.M., Burley, S.K., Chiu, W., Sali, A., Adzhubei, A., Bourne, P.E., Bryant, S.H., Dunbrack, R.L. Jr., Fidelis, K., Frank, J., et al. Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14 (2006), 1211–1217 The recommendation to remove purely in silico models from the PDB is contained in this paper.
19. 19 Haas, J., Roth, S., Arnold, K., Kiefer, F., Schmidt, T., Bordoli, L., Schwede, T., The Protein Model Portal – a comprehensive resource for protein structure and model information. Database (Oxford), 2013, 2013, bat031.
20. 20• Fitzgerald, P.M.D., Westbrook, J.D., Bourne, P.E., McMahon, B., Watenpaugh, K.D., Berman, H.M., 4.5 Macromolecular dictionary (mmCIF). Hall, S.R., McMahon, B., (eds.) International Tables for Crystallography G. Definition and Exchange of Crystallographic Data, 2005, Springer, 295–443 A complete description of the mmCIF data dictionary is contained here.
21. 21 Malfois, M., Svergun, D.I., sasCIF: An Extension of Core Crystallographic Information File for SAS. Journal of Applied Crystallography 33 (2000), 812–816.
22. 22 Westbrook, J., Ito, N., Nakamura, H., Henrick, K., Berman, H.M., PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21 (2005), 988–992.
23. 23• Kinjo, A.R., Suzuki, H., Yamashita, R., Ikegawa, Y., Kudou, T., Igarashi, R., Kengaku, Y., Cho, H., Standley, D.M., Nakagawa, A., et al. Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res 40 (2012), D453–D460 Descriptions of PDBj services are given here as well as the RDF format.
24. 24 Lin, D., Manning, N.O., Jiang, J., Abola, E.E., Stampf, D., Prilusky, J., Sussman, J.L., AutoDep: a web-based system for deposition and validation of macromolecular structural information. Acta Cryst D56 (2000), 828–841.
25. 25 Tagari, M., Tate, J., Swaminathan, G.J., Newman, R., Naim, A., Vranken, W., Kapopoulou, A., Hussain, A., Fillon, J., Henrick, K., et al. E-MSD: improving data deposition and structure quality. Nucleic Acids Res 34 (2006), D287–D290.
26. 26• Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., The Protein Data Bank. Nucleic Acids Res 28 (2000), 235–242 This is the first complete description of the services provided by the RCSB PDB.
27. 27• Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., et al. BioMagResBank. Nucleic Acids Res 36 (2008), D402–D408 A summary of the services provided by BMRB is given here.
28. 28 Drug Design Data Resource Community: Continuous Evaluation of Ligand Pose Prediction. https://drugdesigndata.org/about/celpp (accessed 18.04.16).
29. 29 Rose, P.W., Prlic, A., Bi, C., Bluhm, W.F., Christie, C.H., Dutta, S., Green, R.K., Goodsell, D.S., Westbrook, J.D., Woo, J., et al. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res 43 (2015), D345–D356.
30. 30 Velankar, S., van Ginkel, G., Alhroub, Y., Battle, G.M., Berrisford, J.M., Conroy, M.J., Dana, J.M., Gore, S.P., Gutmanas, A., Haslam, P., et al. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res 44 (2016), D385–D395.
31. 31• Gutmanas, A., Alhroub, Y., Battle, G.M., Berrisford, J.M., Bochet, E., Conroy, M.J., Dana, J.M., Fernandez Montecelo, M.A., van Ginkel, G., Gore, S.P., et al. PDBe: Protein Data Bank in Europe. Nucleic Acids Res 42 (2014), D285–D291 The services offered by PDBe are described.
32. 32 Kinjo, A.R., Nakamura, H., Composite structural motifs of binding sites for delineating biological functions of proteins. PLoS One, 7, 2012, e31437.
33. 33 Markley, J.L., Ulrich, E.L., Berman, H.M., Henrick, K., Nakamura, H., Akutsu, H., BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40 (2008), 153–155.
34. 34 Sillitoe, I., Lewis, T.E., Cuff, A., Das, S., Ashford, P., Dawson, N.L., Furnham, N., Laskowski, R.A., Lee, D., Lees, J.G., et al. CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res 43 (2015), D376–D381.
35. 35 Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J., Chothia, C., Murzin, A.G., SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 32 (2004), D226–D229.
36. 36 Andreeva, A., Howorth, D., Chandonia, J.M., Brenner, S.E., Hubbard, T.J., Chothia, C., Murzin, A.G., Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36 (2008), D419–D425.
37. 37 Lewis, T.E., Sillitoe, I., Andreeva, A., Blundell, T.L., Buchan, D.W., Chothia, C., Cozzetto, D., Dana, J.M., Filippis, I., Gough, J., et al. Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res 43 (2015), D382–D386.
38. 38 Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J.D., Gelbin, A., Demeny, T., Hsieh, S.-h., Srinivasan, A.R., Schneider, B., The Nucleic Acid Database – a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63 (1992), 751–759.
39. 39 Gabanyi, M.J., Adams, P.D., Arnold, K., Bordoli, L., Carter, L.G., Flippen-Andersen, J., Gifford, L., Haas, J., Kouranov, A., McLaughlin, W.A., et al. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genom 12 (2011), 45–54.
40. 40 Madl, T., Gabel, F., Sattler, M., NMR and small-angle scattering-based structural analysis of protein complexes in solution. J Struct Biol 173 (2011), 472–482.
41. 41 Wang, Z., Chernyshev, A., Koehn, E.M., Manuel, T.D., Lesley, S.A., Kohen, A., Oxidase activity of a flavin-dependent thymidylate synthase. FEBS J 276 (2009), 2801–2810.
42. 42 Byeon, I.J., Louis, J.M., Gronenborn, A.M., A captured folding intermediate involved in dimerization and domain-swapping of GB1. J Mol Biol 340 (2004), 615–625.
43. 43 Ward, A.B., Sali, A., Wilson, I.A., Biochemistry. Integrative structural biology. Science 339 (2013), 913–915.
44. 44•• Sali, A., Berman, H.M., Schwede, T., Trewhella, J., Kleywegt, G., Burley, S.K., Markley, J., Nakamura, H., Adams, P., Bonvin, A.M., et al. Outcome of the first wwPDB hybrid/integrative methods task force workshop. Structure 23 (2015), 1156–1167 This paper summarized the steps necessary to establish an archive of structure data from hybrid/integrative methods.