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The Protein Data Bank: Overview and Tools for Drug Discovery

  • Helen M. Berman
  • Peter W. Rose
  • Shuchismita Dutta
  • Christine Zardecki
  • Andreas Prlić
Conference paper
Part of the NATO Science for Peace and Security Series A: Chemistry and Biology book series (NAPSA)

Abstract

The increasing size and complexity of the three dimensional (3D) structures of biomacromolecules in the Protein Data Bank (PDB) is a reflection of the growth in the field of structural biology. Although the PDB archive was initially used only in the field of structural biology, it has grown to become a valuable resource for understanding biology at a molecular level and is critical for designing new therapeutic options for various diseases. The many uses of the PDB archive depend upon on the tools and resources for both data management and for data access and analysis.

Keywords

Protein Data Bank Nuclear Magnetic Resonance Spectroscopy Protein Data Bank Entry Summary Page Water Mediate Hydrogen Bond 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgement

The RCSB PDB is supported by funds from the National Science Foundation (NSF DBI 1338415), National Institutes of Health, and the Department of Energy (DOE). RCSB PDB is a member of the Worldwide Protein Data Bank.

References

  1. 1.
    Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181:662–666CrossRefPubMedGoogle Scholar
  2. 2.
    Kendrew JC, Dickerson RE, Strandberg BE, Hart RG, Davies DR, Phillips DC, Shore VC (1960) Structure of myoglobin: a three-dimensional Fourier synthesis at 2 A. resolution. Nature 185(4711):422–427CrossRefPubMedGoogle Scholar
  3. 3.
    Perutz MF, Rossmann MG, Cullis AF, Muirhead H, Will G, North ACT (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5 Å resolution, obtained by X-ray analysis. Nature 185:416–422CrossRefPubMedGoogle Scholar
  4. 4.
    Bolton W, Perutz MF (1970) Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Ångstrom units resolution. Nature 228(271):551–552CrossRefPubMedGoogle Scholar
  5. 5.
    Berman HM, Kleywegt GJ, Nakamura H, Markley JL (2013) How community has shaped the Protein Data Bank. Structure 21(9):1485–1491CrossRefPubMedGoogle Scholar
  6. 6.
    Berman H (2008) The Protein Data Bank: a historical perspective. Acta Crystallogr A: Found Crystallogr 64:88–95CrossRefGoogle Scholar
  7. 7.
    Protein Data Bank (1971) Protein Data Bank. Nat New Biol 233:223Google Scholar
  8. 8.
    Berman HM, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10(12):980CrossRefPubMedGoogle Scholar
  9. 9.
    Berman HM, Henrick K, Kleywegt G, Nakamura H, Markley J (2012) The worldwide Protein Data Bank. In: Arnold E, Himmel DM, Rossmann MG (eds) International tables for X-ray crystallography, vol F, Crystallography of biological macromolecules. Springer, Dordrecht, pp 827–832CrossRefGoogle Scholar
  10. 10.
    Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W (2011) EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res 39:D456–D464CrossRefPubMedCentralPubMedGoogle Scholar
  11. 11.
    Westbrook J, Henrick K, Ulrich EL, Berman HM (2005) 3.6.2 The Protein Data Bank exchange data dictionary. In: Hall SR, McMahon B (eds) International tables for crystallography, vol G. Definition and exchange of crystallographic data. Springer, Dordrecht, pp 195–198Google Scholar
  12. 12.
    Read RJ, Adams PD, Arendall WB III, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lutteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH (2011) A new generation of crystallographic validation tools for the Protein Data Bank. Structure 19(10):1395–1412CrossRefPubMedCentralPubMedGoogle Scholar
  13. 13.
    Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Markley JL, Richardson J, Schwieters C, Vuister GW, Vranken W, Wishart D (2013) Recommendations of the wwPDB NMR structure validation task force. Structure 21:1563–1570CrossRefPubMedGoogle Scholar
  14. 14.
    Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schroder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL (2012) Outcome of the first electron microscopy validation task force meeting. Structure 20(2):205–214CrossRefPubMedGoogle Scholar
  15. 15.
    Trewhella J, Hendrickson WA, Sato M, Schwede T, Svergun D, Tainer JA, Westbrook J, Kleywegt GJ, Berman HM (2013) Meeting report of the wwPDB small-angle scattering task force: data requirements for biomolecular modeling and the PDB. Structure 21:875–881CrossRefPubMedGoogle Scholar
  16. 16.
    Gore S, Velankar S, Kleywegt GJ (2012) Implementing an X-ray validation pipeline for the Protein Data Bank. Acta Crystallogr D68:478–483Google Scholar
  17. 17.
    Dutta S, Dimitropoulos D, Feng Z, Periskova I, Sen S, Shao C, Westbrook J, Young J, Zhuravleva M, Kleywegt G, Berman H (2013) Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. Biopolymers 101(6):659–668CrossRefGoogle Scholar
  18. 18.
    Berman HM, Westbrook JD, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242CrossRefPubMedCentralPubMedGoogle Scholar
  19. 19.
    Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-Garcia E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ (2014) PDBe: Protein Data Bank in Europe. Nucleic Acids Res 42(1):D285–D291CrossRefPubMedCentralPubMedGoogle Scholar
  20. 20.
    Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H (2012) Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res 40:D453–D460CrossRefPubMedCentralPubMedGoogle Scholar
  21. 21.
    Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408CrossRefPubMedCentralPubMedGoogle Scholar
  22. 22.
    Berman HM, Coimbatore Narayanan B, Costanzo LD, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlic A, Rose PW, Shao C, Yang H, Young J, Zardecki C (2013) Trendspotting in the protein data bank. FEBS Lett 587(8):1036–1045CrossRefPubMedCentralPubMedGoogle Scholar
  23. 23.
    Goodsell DS, Burley SK, Berman HM (2013) Revealing structural views of biology. Biopolymers 99(11):817–824CrossRefPubMedGoogle Scholar
  24. 24.
    Wlodawer A, Miller M, Jaskolski M, Sathyanarayana BK, Baldwin E, Weber IT, Selk LM, Clawson L, Schneider J, Kent SB (1989) Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science 245(4918):616–621CrossRefPubMedGoogle Scholar
  25. 25.
    Wensing AM, van Maarseveen NM, Nijhuis M (2010) Fifteen years of HIV protease inhibitors: raising the barrier to resistance. Antiviral Res 85(1):59–74CrossRefPubMedGoogle Scholar
  26. 26.
    Cihlar T, Ray AS (2010) Nucleoside and nucleotide HIV reverse transcriptase inhibitors: 25 years after zidovudine. Antiviral Res 85(1):39–58CrossRefPubMedGoogle Scholar
  27. 27.
    Yonath A (2005) Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation. Annu Rev Biochem 74:649–679CrossRefPubMedGoogle Scholar
  28. 28.
    Bulkley D, Innis CA, Blaha G, Steitz TA (2010) Revisiting the structures of several antibiotics bound to the bacterial ribosome. Proc Natl Acad Sci U S A 107(40):17158–17163CrossRefPubMedCentralPubMedGoogle Scholar
  29. 29.
    Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne PE (2013) The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res 41(D1):D475–D482CrossRefPubMedCentralPubMedGoogle Scholar
  30. 30.
    Stierand K, Rarey M (2010) Drawing the PDB: protein − ligand complexes in two dimensions. Med Chem Lett 1:540–545CrossRefGoogle Scholar
  31. 31.
    Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS (2011) DrugBank 3.0: a comprehensive resource for ‘omics’ research on drugs. Nucleic Acids Res 39(Database issue):D1035–D1041CrossRefPubMedCentralPubMedGoogle Scholar
  32. 32.
    Young JY, Feng Z, Dimitropoulos D, Sala R, Westbrook J, Zhuravleva M, Shao C, Quesada M, Peisach E, Berman HM (2013) Chemical annotation of small and peptide-like molecules at the Protein Data Bank. Database 2013:bat079Google Scholar
  33. 33.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  34. 34.
    Hopper P, Harrison SC, Sauer RT (1984) Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications. J Mol Biol 177(4):701–713CrossRefPubMedGoogle Scholar
  35. 35.
    Schmeing TM, Voorhees RM, Kelley AC, Gao YG, Murphy FVT, Weir JR, Ramakrishnan V (2009) The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326(5953):688–694CrossRefPubMedCentralPubMedGoogle Scholar
  36. 36.
    Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V (2009) Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 16(5):528–533CrossRefPubMedCentralPubMedGoogle Scholar
  37. 37.
    Gao YG, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V (2009) The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326(5953):694–699CrossRefPubMedCentralPubMedGoogle Scholar
  38. 38.
    Nagar B, Hantschel O, Young MA, Scheffzek K, Veach D, Bornmann W, Clarkson B, Superti-Furga G, Kuriyan J (2003) Structural basis for the autoinhibition of c-Abl tyrosine kinase. Cell 112(6):859–871CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Helen M. Berman
    • 1
  • Peter W. Rose
    • 2
  • Shuchismita Dutta
    • 1
  • Christine Zardecki
    • 1
  • Andreas Prlić
    • 2
  1. 1.RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, RutgersThe State University of New JerseyPiscatawayUSA
  2. 2.RCSB Protein Data Bank, San Diego Supercomputer CenterUniversity of California San DiegoLa JollaUSA

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