Literature DB >> 19082769

Data deposition and annotation at the worldwide protein data bank.

Shuchismita Dutta1, Kyle Burkhardt, Jasmine Young, Ganesh J Swaminathan, Takanori Matsuura, Kim Henrick, Haruki Nakamura, Helen M Berman.   

Abstract

The Protein Data Bank (PDB) is the repository for three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive is free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and general audiences to understand biological phenomenon at a molecular level. Analysis of this structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included.

Mesh:

Substances:

Year:  2008        PMID: 19082769     DOI: 10.1007/s12033-008-9127-7

Source DB:  PubMed          Journal:  Mol Biotechnol        ISSN: 1073-6085            Impact factor:   2.695


  45 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

Authors:  A A Vaguine; J Richelle; S J Wodak
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-01-01

3.  Announcing the worldwide Protein Data Bank.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura
Journal:  Nat Struct Biol       Date:  2003-12

4.  E-MSD: an integrated data resource for bioinformatics.

Authors:  A Golovin; T J Oldfield; J G Tate; S Velankar; G J Barton; H Boutselakis; D Dimitropoulos; J Fillon; A Hussain; J M C Ionides; M John; P A Keller; E Krissinel; P McNeil; A Naim; R Newman; A Pajon; J Pineda; A Rachedi; J Copeland; A Sitnov; S Sobhany; A Suarez-Uruena; G J Swaminathan; M Tagari; S Tromm; W Vranken; K Henrick
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  The Uppsala Electron-Density Server.

Authors:  Gerard J Kleywegt; Mark R Harris; Jin Yu Zou; Thomas C Taylor; Anders Wählby; T Alwyn Jones
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-11-26

Review 6.  Large macromolecular complexes in the Protein Data Bank: a status report.

Authors:  Shuchismita Dutta; Helen M Berman
Journal:  Structure       Date:  2005-03       Impact factor: 5.006

7.  Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy.

Authors:  J L Markley; A Bax; Y Arata; C W Hilbers; R Kaptein; B D Sykes; P E Wright; K Wüthrich
Journal:  J Biomol NMR       Date:  1998-07       Impact factor: 2.835

8.  Phi/psi-chology: Ramachandran revisited.

Authors:  G J Kleywegt; T A Jones
Journal:  Structure       Date:  1996-12-15       Impact factor: 5.006

9.  ProMode: a database of normal mode analyses on protein molecules with a full-atom model.

Authors:  Hiroshi Wako; Masaki Kato; Shigeru Endo
Journal:  Bioinformatics       Date:  2004-04-01       Impact factor: 6.937

10.  Design of a data model for developing laboratory information management and analysis systems for protein production.

Authors:  Anne Pajon; John Ionides; Jon Diprose; Joël Fillon; Rasmus Fogh; Alun W Ashton; Helen Berman; Wayne Boucher; Miroslaw Cygler; Emeline Deleury; Robert Esnouf; Joël Janin; Rosalind Kim; Isabelle Krimm; Catherine L Lawson; Eric Oeuillet; Anne Poupon; Stéphane Raymond; Tim Stevens; Herman van Tilbeurgh; John Westbrook; Peter Wood; Eldon Ulrich; Wim Vranken; Li Xueli; Ernest Laue; David I Stuart; Kim Henrick
Journal:  Proteins       Date:  2005-02-01
View more
  54 in total

Review 1.  Inference of functional properties from large-scale analysis of enzyme superfamilies.

Authors:  Shoshana D Brown; Patricia C Babbitt
Journal:  J Biol Chem       Date:  2011-11-08       Impact factor: 5.157

2.  Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.

Authors:  Gurmukh Sahota; Gary D Stormo
Journal:  Bioinformatics       Date:  2010-08-31       Impact factor: 6.937

3.  Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure.

Authors:  Ryan Day; Kristin P Lennox; David B Dahl; Marina Vannucci; Jerry W Tsai
Journal:  Bioinformatics       Date:  2010-11-02       Impact factor: 6.937

4.  Evolution of cyclic amidohydrolases: a highly diversified superfamily.

Authors:  Matthieu Barba; Nicolas Glansdorff; Bernard Labedan
Journal:  J Mol Evol       Date:  2013-08-27       Impact factor: 2.395

Review 5.  Coverage of protein domain families with structural protein-protein interactions: current progress and future trends.

Authors:  Alexander Goncearenco; Benjamin A Shoemaker; Dachuan Zhang; Alexey Sarychev; Anna R Panchenko
Journal:  Prog Biophys Mol Biol       Date:  2014-06-13       Impact factor: 3.667

6.  Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes.

Authors:  Matteo Citarelli; Sachin Teotia; Rebecca S Lamb
Journal:  BMC Evol Biol       Date:  2010-10-13       Impact factor: 3.260

7.  Ligands in PSI structures.

Authors:  Abhinav Kumar; Hsiu Ju Chiu; Herbert L Axelrod; Andrew Morse; Marc André Elsliger; Ian A Wilson; Ashley Deacon
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2010-07-06

8.  The MiST2 database: a comprehensive genomics resource on microbial signal transduction.

Authors:  Luke E Ulrich; Igor B Zhulin
Journal:  Nucleic Acids Res       Date:  2009-11-09       Impact factor: 16.971

9.  MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets.

Authors:  Vineet K Sharma; Naveen Kumar; Tulika Prakash; Todd D Taylor
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971

Review 10.  From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.

Authors:  Ursula Hinz
Journal:  Cell Mol Life Sci       Date:  2009-12-31       Impact factor: 9.261

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.