Literature DB >> 33950382

The Protein Data Bank Archive.

Sameer Velankar1, Stephen K Burley2,3,4,5, Genji Kurisu6, Jeffrey C Hoch7, John L Markley8.   

Abstract

Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open access data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners-the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu ). The PDB archive currently includes ~175,000 entries. The wwPDB has established a number of task forces and working groups that bring together experts form the community who provide recommendations on improving data standards and data validation for improving data quality and integrity. The wwPDB members continue to develop the joint deposition, biocuration, and validation system (OneDep) to improve data quality and accommodate new data from emerging techniques such as 3DEM. Each PDB entry contains coordinate model and associated metadata for all experimentally determined atomic structures, experimental data for the traditional structure determination techniques (X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy), validation reports, and additional information on quaternary structures. The wwPDB partners are committed to following the FAIR (Findability, Accessibility, Interoperability, and Reproducibility) principles and have implemented a DOI resolution mechanism that provides access to all the relevant files for a given PDB entry. On average, >250 new entries are added to the archive every week and made available by each wwPDB partner via FTP area. The wwPDB partner sites also develop data access and analysis tools and make these available via their websites. wwPDB continues to work with experts in the community to establish a federation of archives for archiving structures determined using integrative/hybrid method where multiple experimental techniques are used.

Keywords:  3DEM; Biocuration, and Validation system OneDep; Deposition; Integrative hybrid methods; Macromolecular structure archive; NMR spectroscopy; PDBx/mmCIF; Protein Data Bank; Validation task forces; Worldwide Protein Data Bank (wwPDB); X-ray crystallography

Year:  2021        PMID: 33950382     DOI: 10.1007/978-1-0716-1406-8_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  57 in total

1.  Announcing the worldwide Protein Data Bank.

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

2.  A three-dimensional model of the myoglobin molecule obtained by x-ray analysis.

Authors:  J C KENDREW; G BODO; H M DINTZIS; R G PARRISH; H WYCKOFF; D C PHILLIPS
Journal:  Nature       Date:  1958-03-08       Impact factor: 49.962

3.  Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.

Authors:  J D WATSON; F H CRICK
Journal:  Nature       Date:  1953-04-25       Impact factor: 49.962

4.  Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis.

Authors:  M F PERUTZ; M G ROSSMANN; A F CULLIS; H MUIRHEAD; G WILL; A C NORTH
Journal:  Nature       Date:  1960-02-13       Impact factor: 49.962

Review 5.  How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals.

Authors:  John D Westbrook; Stephen K Burley
Journal:  Structure       Date:  2018-12-27       Impact factor: 5.006

Review 6.  RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.

Authors:  Stephen K Burley; Helen M Berman; Cole Christie; Jose M Duarte; Zukang Feng; John Westbrook; Jasmine Young; Christine Zardecki
Journal:  Protein Sci       Date:  2017-11-11       Impact factor: 6.725

7.  New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).

Authors:  Akira R Kinjo; Gert-Jan Bekker; Hiroshi Wako; Shigeru Endo; Yuko Tsuchiya; Hiromu Sato; Hafumi Nishi; Kengo Kinoshita; Hirofumi Suzuki; Takeshi Kawabata; Masashi Yokochi; Takeshi Iwata; Naohiro Kobayashi; Toshimichi Fujiwara; Genji Kurisu; Haruki Nakamura
Journal:  Protein Sci       Date:  2017-09-18       Impact factor: 6.725

8.  PDBe: improved findability of macromolecular structure data in the PDB.

Authors:  David R Armstrong; John M Berrisford; Matthew J Conroy; Aleksandras Gutmanas; Stephen Anyango; Preeti Choudhary; Alice R Clark; Jose M Dana; Mandar Deshpande; Roisin Dunlop; Paul Gane; Romana Gáborová; Deepti Gupta; Pauline Haslam; Jaroslav Koča; Lora Mak; Saqib Mir; Abhik Mukhopadhyay; Nurul Nadzirin; Sreenath Nair; Typhaine Paysan-Lafosse; Lukas Pravda; David Sehnal; Osman Salih; Oliver Smart; James Tolchard; Mihaly Varadi; Radka Svobodova-Vařeková; Hossam Zaki; Gerard J Kleywegt; Sameer Velankar
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

9.  BioMagResBank.

Authors:  Eldon L Ulrich; Hideo Akutsu; Jurgen F Doreleijers; Yoko Harano; Yannis E Ioannidis; Jundong Lin; Miron Livny; Steve Mading; Dimitri Maziuk; Zachary Miller; Eiichi Nakatani; Christopher F Schulte; David E Tolmie; R Kent Wenger; Hongyang Yao; John L Markley
Journal:  Nucleic Acids Res       Date:  2007-11-04       Impact factor: 16.971

10.  RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.

Authors:  Stephen K Burley; Helen M Berman; Charmi Bhikadiya; Chunxiao Bi; Li Chen; Luigi Di Costanzo; Cole Christie; Ken Dalenberg; Jose M Duarte; Shuchismita Dutta; Zukang Feng; Sutapa Ghosh; David S Goodsell; Rachel K Green; Vladimir Guranovic; Dmytro Guzenko; Brian P Hudson; Tara Kalro; Yuhe Liang; Robert Lowe; Harry Namkoong; Ezra Peisach; Irina Periskova; Andreas Prlic; Chris Randle; Alexander Rose; Peter Rose; Raul Sala; Monica Sekharan; Chenghua Shao; Lihua Tan; Yi-Ping Tao; Yana Valasatava; Maria Voigt; John Westbrook; Jesse Woo; Huanwang Yang; Jasmine Young; Marina Zhuravleva; Christine Zardecki
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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Review 5.  Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.

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  7 in total

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