Literature DB >> 27450113

The archiving and dissemination of biological structure data.

Helen M Berman1, Stephen K Burley2, Gerard J Kleywegt3, John L Markley4, Haruki Nakamura5, Sameer Velankar3.   

Abstract

The global Protein Data Bank (PDB) was the first open-access digital archive in biology. The history and evolution of the PDB are described, together with the ways in which molecular structural biology data and information are collected, curated, validated, archived, and disseminated by the members of the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org). Particular emphasis is placed on the role of community in establishing the standards and policies by which the PDB archive is managed day-to-day.
Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

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Year:  2016        PMID： 27450113      PMCID： PMC5161703          DOI： 10.1016/j.sbi.2016.06.018

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN： 0959-440X            Impact factor:   6.809


  37 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.  Announcing the worldwide Protein Data Bank.

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

3.  Escape from lysosomes.

Authors: 
Journal:  Nat New Biol       Date:  1971-10-20

4.  Recommendations of the wwPDB NMR Validation Task Force.

Authors:  Gaetano T Montelione; Michael Nilges; Ad Bax; Peter Güntert; Torsten Herrmann; Jane S Richardson; Charles D Schwieters; Wim F Vranken; Geerten W Vuister; David S Wishart; Helen M Berman; Gerard J Kleywegt; John L Markley
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

5.  Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Angstrom units resolution.

Authors:  W Bolton; M F Perutz
Journal:  Nature       Date:  1970-11-07       Impact factor: 49.962

6.  The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

Authors:  Margaret J Gabanyi; Paul D Adams; Konstantin Arnold; Lorenza Bordoli; Lester G Carter; Judith Flippen-Andersen; Lida Gifford; Juergen Haas; Andrei Kouranov; William A McLaughlin; David I Micallef; Wladek Minor; Raship Shah; Torsten Schwede; Yi-Ping Tao; John D Westbrook; Matthew Zimmerman; Helen M Berman
Journal:  J Struct Funct Genomics       Date:  2011-04-07

7.  Outcome of the first electron microscopy validation task force meeting.

Authors:  Richard Henderson; Andrej Sali; Matthew L Baker; Bridget Carragher; Batsal Devkota; Kenneth H Downing; Edward H Egelman; Zukang Feng; Joachim Frank; Nikolaus Grigorieff; Wen Jiang; Steven J Ludtke; Ohad Medalia; Pawel A Penczek; Peter B Rosenthal; Michael G Rossmann; Michael F Schmid; Gunnar F Schröder; Alasdair C Steven; David L Stokes; John D Westbrook; Willy Wriggers; Huanwang Yang; Jasmine Young; Helen M Berman; Wah Chiu; Gerard J Kleywegt; Catherine L Lawson
Journal:  Structure       Date:  2012-02-08       Impact factor: 5.006

8.  The Protein Model Portal--a comprehensive resource for protein structure and model information.

Authors:  Juergen Haas; Steven Roth; Konstantin Arnold; Florian Kiefer; Tobias Schmidt; Lorenza Bordoli; Torsten Schwede
Journal:  Database (Oxford)       Date:  2013-04-26       Impact factor: 3.451

9.  Genome3D: exploiting structure to help users understand their sequences.

Authors:  Tony E Lewis; Ian Sillitoe; Antonina Andreeva; Tom L Blundell; Daniel W A Buchan; Cyrus Chothia; Domenico Cozzetto; José M Dana; Ioannis Filippis; Julian Gough; David T Jones; Lawrence A Kelley; Gerard J Kleywegt; Federico Minneci; Jaina Mistry; Alexey G Murzin; Bernardo Ochoa-Montaño; Matt E Oates; Marco Punta; Owen J L Rackham; Jonathan Stahlhacke; Michael J E Sternberg; Sameer Velankar; Christine Orengo
Journal:  Nucleic Acids Res       Date:  2014-10-27       Impact factor: 16.971

10.  PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

Authors:  Sameer Velankar; Glen van Ginkel; Younes Alhroub; Gary M Battle; John M Berrisford; Matthew J Conroy; Jose M Dana; Swanand P Gore; Aleksandras Gutmanas; Pauline Haslam; Pieter M S Hendrickx; Ingvar Lagerstedt; Saqib Mir; Manuel A Fernandez Montecelo; Abhik Mukhopadhyay; Thomas J Oldfield; Ardan Patwardhan; Eduardo Sanz-García; Sanchayita Sen; Robert A Slowley; Michael E Wainwright; Mandar S Deshpande; Andrii Iudin; Gaurav Sahni; Jose Salavert Torres; Miriam Hirshberg; Lora Mak; Nurul Nadzirin; David R Armstrong; Alice R Clark; Oliver S Smart; Paul K Korir; Gerard J Kleywegt
Journal:  Nucleic Acids Res       Date:  2015-10-17       Impact factor: 16.971
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  18 in total

1.  Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources.

Authors:  Pierre Aller; Allen M Orville
Journal:  Methods Mol Biol       Date:  2021

2.  COSMIC-3D provides structural perspectives on cancer genetics for drug discovery.

Authors:  Harry C Jubb; Harpreet K Saini; Marcel L Verdonk; Simon A Forbes
Journal:  Nat Genet       Date:  2018-09       Impact factor: 38.330

3.  Computational Resources for the Interpretation of Variations in Cancer.

Authors:  Grete Francesca Privitera; Salvatore Alaimo; Alfredo Ferro; Alfredo Pulvirenti
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 2.622

Review 4.  Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

Authors:  Rebecca J Howard; Vincenzo Carnevale; Lucie Delemotte; Ute A Hellmich; Brad S Rothberg
Journal:  Biochim Biophys Acta Biomembr       Date:  2017-12-16       Impact factor: 4.019

5.  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

6.  Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.

Authors:  Akira R Kinjo; Gert-Jan Bekker; Hirofumi Suzuki; Yuko Tsuchiya; Takeshi Kawabata; Yasuyo Ikegawa; Haruki Nakamura
Journal:  Nucleic Acids Res       Date:  2016-10-26       Impact factor: 16.971

7.  Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Authors:  Gemma L Holliday; Shoshana D Brown; Eyal Akiva; David Mischel; Michael A Hicks; John H Morris; Conrad C Huang; Elaine C Meng; Scott C-H Pegg; Thomas E Ferrin; Patricia C Babbitt
Journal:  Database (Oxford)       Date:  2017-01-01       Impact factor: 3.451

8.  Data archiving and availability in an era of open science.

Authors:  Edward N Baker
Journal:  IUCrJ       Date:  2017-01-01       Impact factor: 4.769

9.  R3D-BLAST2: an improved search tool for similar RNA 3D substructures.

Authors:  Ching-Yu Yen; Jian-Cheng Lin; Kun-Tze Chen; Chin Lung Lu
Journal:  BMC Bioinformatics       Date:  2017-12-28       Impact factor: 3.169

Review 10.  Where is crystallography going?

Authors:  Jonathan M Grimes; David R Hall; Alun W Ashton; Gwyndaf Evans; Robin L Owen; Armin Wagner; Katherine E McAuley; Frank von Delft; Allen M Orville; Thomas Sorensen; Martin A Walsh; Helen M Ginn; David I Stuart
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-02-01       Impact factor: 7.652
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