The RCSB protein data bank: Integrative view of protein, gene and 3D structural information

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D271-D281

  Rose, Peter W ^a   Prlić, Andreas ^a   Altunkaya, Ali ^a   Bi, Chunxiao ^a   Bradley, Anthony R ^a   Christie, Cole H ^a   Di Costanzo, Luigi ^b   Duarte, Jose M ^a   Dutta, Shuchismita ^b   Feng, Zukang ^b   Green, Rachel Kramer ^b   Goodsell, David S ^b,c   Hudson, Brian ^b   Kalro, Tara ^a   Lowe, Robert ^b   Peisach, Ezra ^b   Randle, Christopher ^a   Rose, Alexander S ^a   Shao, Chenghua ^b   Tao, Yi Ping ^b   Valasatava, Yana ^a   Voigt, Maria ^b   Westbrook, John D ^b   Woo, Jesse ^a   Yang, Huangwang ^b   Young, Jasmine Y ^b   Zardecki, Christine ^b   Berman, Helen M ^b   Burley, Stephen K ^a,b,d,e   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

^e UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; CHROMOSOME POSITIONING; CONTROLLED STUDY; GENE STRUCTURE; HUMAN; HUMAN GENOME; METABOLISM; PROTEIN DATA BANK; PROTEIN MODIFICATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; BIOLOGY; CHEMISTRY; COMPUTER INTERFACE; GENETIC DATABASE; GENETICS; INFORMATION PROCESSING; MOLECULAR MODEL; PROCEDURES; PROTEIN CONFORMATION; SOFTWARE; STRUCTURE ACTIVITY RELATION; WEB BROWSER;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATASETS AS TOPIC; METABOLIC NETWORKS AND PATHWAYS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; USER-COMPUTER INTERFACE; WEB BROWSER;

EID: 85016111024     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: None     Document Type: Article

References (39)

1. Berman, H.M.,Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E.(2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
2. Rose, P.W., Prlíc, A., Bi, C., Bluhm, W.F., Christie, C.H., Dutta, S., Green, R.K., Goodsell, D.S., Westbrook, J.D.,Woo, J.et al. (2015) The RCSB Protein Data Bank: Views of structural biology for basic and applied research and education. Nucleic Acids Res., 43, D345-D356.
3. Berman, H., Henrick, K.and Nakamura, H.(2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980.
4. Kinjo, A.R., Suzuki, H., Yamashita, R., Ikegawa, Y., Kudou, T., Igarashi, R., Kengaku, Y., Cho, H., Standley, D.M., Nakagawa, A.et al. (2012) Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format. Nucleic Acids Res., 40, D453-D460.
5. 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. (2016) PDBe: improved accessibility of macromolecular structure data from PDB and EMD B.Nucleic Acids Res., 44, D385-D395.
6. 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. (2008) BioMagResBank. Nucleic Acids Res., 36, D402-D408.
7. Rose, P.W., Bi, C., Bluhm, W.F., Christie, C.H., Dimitropoulos, D., Dutta, S., Green, R.K., Goodsell, D.S., Prlíc, A., Quesada, M.et al. (2013) The RCSB Protein Data Bank: New resources for research and education. Nucleic Acids Res., 41, D475-D482.
8. Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlíc, A., Quesada, M., Quinn, G.B., Westbrook, J.D.et al. (2011) The RCSB Protein Data Bank: Redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
9. Goodsell, D.S. (2010) The Protein Data Bank: exploring biomolecular structure. Nat. Educ., 3, 39.
10. Berman, H.M., Coimbatore Narayanan, B., Costanzo Di, L., Dutta, S., Ghosh, S., Hudson, B.P., Lawson, C.L., Peisach, E., Prlíc, A., Rose, P.W. et al. (2013) Trendspotting in the Protein Data Bank. FEBS Lett., 587, 1036-1045.
11. Berman, H.M., Rose, P.W., Dutta, S., Zardecki, C.and Prlíc, A.(2015) The protein data bank: overview and tools for drug discovery. In: Multifaceted Roles of Crystallography in Modern Drug Discovery. Springer, Netherlands, pp. 93-106.
12. O'Donoghue, S.I., Goodsell, D.S., Frangakis, A.S., Jossinet, F., Laskowski, R.A., Nilges, M., Saibil, H.R., Schafferhans, A., Wade, R.C., Westhof, E.et al. (2010) Visualization of macromolecular structures. Nat. Methods, 7, S42-S55.
13. Pirhadi, S., Sunseri, J.and Koes, D.R. (2016) Open source molecular modeling. J.Mol. Graph. Model., doi:10.1016/j.jmgm.2016.07.008.
14. Biasini, M.(2015) Zenodo. doi:10.5281/zenodo.20980.
15. Rose, A.S. and Hildebrand, P.W. (2015) NGL Viewer: a web application for molecular visualization. Nucleic Acids Res., 43, W576-W579.
16. Rose, A.S., Bradley, A.R., Valasatava, Y., Duarte, J.M., Prlíc, A.and Rose, P.W. (2016) Web-based molecular graphics for large complexes. In: Proceedings of the 21st International Conference on Web3D Technology-Web3D '16. ACM Press, NY, pp. 185-186.
17. Prlíc, A., Kalro, T., Bhattacharya, R., Christie, C., Burley, S.K.and Rose, P.W. (2016) Integrating Genomic information with protein sequence and 3D atomic level structure at the RCSB Protein Data Bank. Bioinformatics, doi:10.1093/bioinformatics/btw547.
18. Garavelli, J.S. (1999) The RESID Database of protein structure modifications. Nucleic Acids Res., 27, 198-199.
19. Garavelli, J.S. (2000) The RESID Database of protein structure modifications: 2000 update. Nucleic Acids Res., 28, 209-211.
20. Montecchi-Palazzi, L., Beavis, R., Binz, P.-A., Chalkley, R.J., Cottrell, J., Creasy, D., Shofstahl, J., Seymour, S.L.and Garavelli, J.S. (2008) The PSI-MOD community standard for representation of protein modification data. Nat. Biotechnol., 26, 864-866.
21. Prlíc, A., Yates, A., Bliven, S.E., Rose, P.W., Jacobsen, J., Troshin, P.U., Chapman, M., Gao, J., Koh, C.H., Foisy, S.et al. (2012) BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 28, 2693-2695.
22. Zhang, Y., Thiele, I., Weekes, D., Li, Z., Jaroszewski, L., Ginalski, K., Deacon, A.M., Wooley, J., Lesley, S.A., Wilson, I.A.et al. (2009) Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 325, 1544-1549.
23. King, Z.A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N.E.and Palsson, B.O. (2015) Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS Comput. Biol., 11, e1004321.
24. Brunk, E., Mih, N., Monk, J., Zhang, Z., O'Brien, E.J., Bliven, S.E., Chen, K., Chang, R.L., Bourne, P.E.and Palsson, B.O. (2016) Systems biology of the structural proteome. BMC Syst. Biol., 10, 26.
25. King, Z.A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J.A., Ebrahim, A., Palsson, B.O. and Lewis, N.E.(2016) BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res., 44, D515-D522.
26. Velankar, S., Dana, J.M., Jacobsen, J., Van Ginkel, G., Gane, P.J., Luo, J., Oldfield, T.J., O'Donovan, C., Martin, M.J.and Kleywegt, G.J. (2013) SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res., 41, D483-D489.
27. The UniProt Consortium (2014) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
28. Huang, Y.-H., Rose, P.W. and Hsu, C.-N. (2015) Citing a Data Repository: a case study of the Protein Data Bank. PLoS One, 10, e0136631.
29. Read, R.J., Adams, P.D., Arendall, W.B.III, Brunger, A.T., Emsley, P., Joosten, R.P., Kleywegt, G.J., Krissinel, E.B., Lütteke, T., Otwinowski, Z.et al. (2011) A new generation of crystallographic validation tools for the Protein Data Bank. Structure, 19, 1395-1412.
30. 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. (2013) Recommendations of the wwPDB NMR validation task force. Structure, 21, 1563-1570.
31. 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. (2016) Outcome of the first electron microscopy validation task force meeting. Structure, 20, 205-214.
32. Read, R.J.(1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A, 42, 140-149.
33. Meyer, P.A., Socias, S., Key, J., Ransey, E., Tjon, E.C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D.et al. (2016) Data publication with the structural biology data grid supports live analysis. Nat. Commun., 7, 10882.
34. Androulakis, S., Schmidberger, J., Bate, M.A., DeGori, R., Beitz, A., Keong, C., Cameron, B.,McGowan, S., Porter, C.J., Harrison, A.et al. (2008) Federated repositories of X-ray diffraction images. Acta Crystallogr. D Biol. Crystallogr., 64, 810-814.
35. Westbrook, J.D., Shao, C., Feng, Z., Zhuravleva, M., Velankar, S.and Young, J.(2015) The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. Bioinformatics, 31, 1274-1278.
36. Young, J.Y., Feng, Z., Dimitropoulos, D., Sala, R., Westbrook, J., Zhuravleva, M., Shao, C., Quesada, M., Peisach, E.and Berman, H.M. (2013) Chemical annotation of small and peptide-like molecules at the Protein Data Bank. Database, 2013, bat079.
37. Dutta, S., Dimitropoulos, D., Feng, Z., Persikova, I., Sen, S., Shao, C., Westbrook, J., Young, J., Zhuravleva, M.A., Kleywegt, G.J. et al. (2014) Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. Biopolymers, 101, 659-668.
38. Zardecki, C., Dutta, S., Goodsell, D.S., Voigt, M.and Burley, S.K.(2016) RCSB Protein Data Bank: A resource for chemical, biochemical, and structural explorations of large and small biomolecules. J.Chem. Educ., 93, 569-575.
39. Goodsell, D.S., Dutta, S., Zardecki, C., Voigt, M., Berman, H.M. and Burley, S.K.(2015) The RCSB PDB 'Molecule of the Month': Inspiring a molecular view of biology. PLoS Biol., 13, e1002140.