Trendspotting in the Protein Data Bank

The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85 000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever‐growing amount of PDB data.

[1]  K. Flaherty,et al.  Three-dimensional structure of a hammerhead ribozyme , 1994, Nature.

[2]  John E. Johnson,et al.  Structural biology of viruses by the combination of electron cryomicroscopy and X-ray crystallography. , 2002, Biochemistry.

[3]  C. Cambillau,et al.  Interaction of a legume lectin with two components of the bacterial cell wall. A crystallographic study. , 1994, Journal of Biological Chemistry.

[4]  N. Seeman,et al.  The general structure of transfer RNA molecules. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Helen M. Berman,et al.  The Worldwide Protein Data Bank , 2012 .

[6]  Crystal Structures of Actinomycin D and Actinomycin Z3. , 1998, Angewandte Chemie.

[7]  B. Hingerty,et al.  Further refinement of the structure of yeast tRNAPhe. , 1978, Journal of molecular biology.

[8]  Gaetano T. Montelione,et al.  The Protein Structure Initiative: achievements and visions for the future , 2012, F1000 biology reports.

[9]  Tomohisa Ogawa,et al.  Structure of rhamnose-binding lectin CSL3: unique pseudo-tetrameric architecture of a pattern recognition protein. , 2009, Journal of molecular biology.

[10]  Haruki Nakamura,et al.  Remediation of the protein data bank archive , 2007, Nucleic Acids Res..

[11]  H. Berman.  Creating a community resource for protein science , 2012, Protein science : a publication of the Protein Society.

[12]  Seung-Gu Kang,et al.  Directing noble metal ion chemistry within a designed ferritin protein. , 2008, Biochemistry.

[13]  D. V. van Aalten,et al.  Structure of Human Chitotriosidase , 2002, The Journal of Biological Chemistry.

[14]  J. Halpert,et al.  Structures of cytochrome P450 2B4 complexed with the antiplatelet drugs ticlopidine and clopidogrel . , 2010, Biochemistry.

[15]  Mathieu Bastian,et al.  Gephi: An Open Source Software for Exploring and Manipulating Networks , 2009, ICWSM.

[16]  M. Rossmann,et al.  The Refinement of Southern Bean Mosaic Virus in Reciprocal Space , 1984 .

[17]  Florent Cipriani,et al.  Improving diffraction by humidity control: a novel device compatible with X-ray beamlines. , 2009, Acta crystallographica. Section D, Biological crystallography.

[18]  U. Linne,et al.  Chemical engineering of Mycobacterium tuberculosis dodecin hybrids. , 2011, Chemical communications.

[19]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[20]  T A Jones,et al.  Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution. , 1984, Journal of molecular biology.

[21]  John D. Westbrook,et al.  Representation of viruses in the remediated PDB archive , 2008, Acta crystallographica. Section D, Biological crystallography.

[22]  D. Rice,et al.  Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution. , 1997, Journal of molecular biology.

[23]  R. Sauer,et al.  Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications. , 1984, Journal of molecular biology.

[24]  Peter G Stockley,et al.  Construction and crystal structure of recombinant STNV capsids. , 2011, Journal of molecular biology.

[25]  M Ptashne,et al.  Recognition of a DNA operator by the repressor of phage 434: a view at high resolution , 1988, Science.

[26]  M G Rossmann,et al.  The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure. , 1988, Acta crystallographica. Section A, Foundations of crystallography.

[27]  Zukang Feng,et al.  The wwPDB common tool for deposition and annotation , 2011 .

[28]  D. Filman,et al.  Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus. , 1989, The EMBO journal.

[29]  S. Harrison,et al.  Structure of tomato bushy stunt virus. II. Comparison of results obtained by electron microscopy and x-ray diffraction. , 1975, Journal of molecular biology.

[30]  Carolyn R. Bertozzi,et al.  Essentials of Glycobiology , 1999 .

[31]  G J Barton,et al.  Deposition of macromolecular structures. , 1998, Acta crystallographica. Section D, Biological crystallography.

[32]  T. Hahn.  International tables for crystallography , 2002 .

[33]  Sébastien Boutet,et al.  Room temperature femtosecond X-ray diffraction of photosystem II microcrystals , 2012, Proceedings of the National Academy of Sciences.

[34]  R. Micura,et al.  Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site. , 2008, Angewandte Chemie.

[35]  Z. Zhou,et al.  Atomic resolution cryo electron microscopy of macromolecular complexes. , 2011, Advances in protein chemistry and structural biology.

[36]  John D. Westbrook,et al.  The PDB Format, mmCIF Formats, and Other Data Formats , 2005 .

[37]  Akira R. Kinjo,et al.  Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format , 2011, Nucleic Acids Res..

[38]  John D. Westbrook,et al.  EMDataBank.org: unified data resource for CryoEM , 2010, Nucleic Acids Res..

[39]  Haruki Nakamura,et al.  BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions , 2008, Journal of biomolecular NMR.

[40]  Sameer Velankar,et al.  PDBe: Protein Data Bank in Europe , 2009, Nucleic Acids Res..

[41]  Zhiyong Lu,et al.  PubMed and beyond: a survey of web tools for searching biomedical literature , 2011, Database J. Biol. Databases Curation.

[42]  L. Prade,et al.  Human renin in complex with remikiren , 2008 .

[43]  Randy J. Read,et al.  A New Generation of Crystallographic Validation Tools for the Protein Data Bank , 2011, Structure.

[44]  H. Berman.  The Protein Data Bank: a historical perspective. , 2008, Acta crystallographica. Section A, Foundations of crystallography.

[45]  Paul D. Adams,et al.  Crystal Structures of a Group II Chaperonin Reveal the Open and Closed States Associated with the Protein Folding Cycle*♦ , 2010, The Journal of Biological Chemistry.

[46]  A. Ferré-D’Amaré,et al.  Crystal structure of a hepatitis delta virus ribozyme , 1998, Nature.

[47]  J. Deisenhofer,et al.  Structural Mechanism for Statin Inhibition of HMG-CoA Reductase , 2001, Science.

[48]  A Klug,et al.  Atomic co-ordinates for yeast phenylalanine tRNA. , 1975, Nucleic acids research.

[49]  R. Shafer,et al.  The three-dimensional structure of the 4:1 mithramycin:d(ACCCGGGT)(2) complex: evidence for an interaction between the E saccharides. , 2000, Biopolymers.

[50]  James A. Ibers,et al.  International tables for X-ray crystallography , 1962 .

[51]  Duilio Cascio,et al.  Structure of a 16-nm Cage Designed by Using Protein Oligomers , 2012, Science.

[52]  Jacques H. van Boom,et al.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution , 1979, Nature.

[53]  M. Baker,et al.  Outcome of the First Electron Microscopy Validation Task Force Meeting , 2012, Structure.

[54]  Structure of human chitotriosidase , 2003 .

[55]  Wah Chiu,et al.  Near-atomic-resolution cryo-EM for molecular virology. , 2011, Current opinion in virology.

[56]  Zukang Feng,et al.  Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank , 2014, Biopolymers.

[57]  M. Rossmann,et al.  Ab initio phase determination and phase extension using non-crystallographic symmetry. , 1995, Current opinion in structural biology.

[58]  M. Hatada,et al.  Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere. , 1991, Journal of medicinal chemistry.

[59]  Timothy S Baker,et al.  The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[60]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[61]  D. Baker,et al.  Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy , 2012, Science.

[62]  C. Abad-Zapatero,et al.  Notes of a protein crystallographer: on the high-resolution structure of the PDB growth rate. , 2012, Acta crystallographica. Section D, Biological crystallography.

[63]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[64]  H R Drew,et al.  Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.