Literature DB >> 26840827

Safeguarding Structural Data Repositories against Bad Apples.

Wladek Minor1, Zbigniew Dauter2, John R Helliwell3, Mariusz Jaskolski4, Alexander Wlodawer5.   

Abstract

Structural biology research generates large amounts of data, some deposited in public databases or repositories, but a substantial remainder never becomes available to the scientific community. In addition, some of the deposited data contain less or more serious errors that may bias the results of data mining. Thorough analysis and discussion of these problems is needed to ameliorate this situation. This perspective is an attempt to propose some solutions and encourage both further discussion and action on the part of the relevant organizations, in particular the PDB and various bodies of the International Union of Crystallography.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 26840827      PMCID: PMC4743038          DOI: 10.1016/j.str.2015.12.010

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  24 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.  Drug development: Raise standards for preclinical cancer research.

Authors:  C Glenn Begley; Lee M Ellis
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

3.  Retraction of "Structure of MsbA from Vibrio cholera: a multidrug resistance ABC transporter homolog in a closed conformation" [J. Mol. Biol. (2003) 330 419-430].

Authors:  Geoffrey Chang
Journal:  J Mol Biol       Date:  2007-06-01       Impact factor: 5.469

4.  Data mining of metal ion environments present in protein structures.

Authors:  Heping Zheng; Maksymilian Chruszcz; Piotr Lasota; Lukasz Lebioda; Wladek Minor
Journal:  J Inorg Biochem       Date:  2008-05-28       Impact factor: 4.155

5.  Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data.

Authors:  Jongkeun Choi; Jae Kyung Chon; Sangsoo Kim; Whanchul Shin
Journal:  Proteins       Date:  2008-02-15

6.  Believe it or not: how much can we rely on published data on potential drug targets?

Authors:  Florian Prinz; Thomas Schlange; Khusru Asadullah
Journal:  Nat Rev Drug Discov       Date:  2011-08-31       Impact factor: 84.694

Review 7.  Unmet challenges of structural genomics.

Authors:  Maksymilian Chruszcz; Marcin Domagalski; Tomasz Osinski; Alexander Wlodawer; Wladek Minor
Journal:  Curr Opin Struct Biol       Date:  2010-08-31       Impact factor: 6.809

8.  Room-temperature X-ray diffraction studies of cisplatin and carboplatin binding to His15 of HEWL after prolonged chemical exposure.

Authors:  Simon W M Tanley; Antoine M M Schreurs; Loes M J Kroon-Batenburg; John R Helliwell
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-10-26

9.  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

10.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
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  22 in total

1.  Prior knowledge or freedom of interpretation? A critical look at a recently published classification of "novel" Zn binding sites.

Authors:  Joanna E Raczynska; Alexander Wlodawer; Mariusz Jaskolski
Journal:  Proteins       Date:  2016-03-10

Review 2.  Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity.

Authors:  Huilin Wang; Liubin Feng; Geoffrey I Webb; Lukasz Kurgan; Jiangning Song; Donghai Lin
Journal:  Brief Bioinform       Date:  2018-09-28       Impact factor: 11.622

3.  A public database of macromolecular diffraction experiments.

Authors:  Marek Grabowski; Karol M Langner; Marcin Cymborowski; Przemyslaw J Porebski; Piotr Sroka; Heping Zheng; David R Cooper; Matthew D Zimmerman; Marc André Elsliger; Stephen K Burley; Wladek Minor
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-10-28       Impact factor: 7.652

Review 4.  A close look onto structural models and primary ligands of metallo-β-lactamases.

Authors:  Joanna E Raczynska; Ivan G Shabalin; Wladek Minor; Alexander Wlodawer; Mariusz Jaskolski
Journal:  Drug Resist Updat       Date:  2018-08-25       Impact factor: 18.500

5.  Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.

Authors:  Przemyslaw J Porebski; Piotr Sroka; Heping Zheng; David R Cooper; Wladek Minor
Journal:  Protein Sci       Date:  2017-09-13       Impact factor: 6.725

6.  Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment.

Authors:  Ivan G Shabalin; Przemyslaw J Porebski; Wladek Minor
Journal:  Crystallogr Rev       Date:  2018-09-21       Impact factor: 2.467

7.  Molstack: A platform for interactive presentations of electron density and cryo-EM maps and their interpretations.

Authors:  Przemyslaw J Porebski; Grzegorz Bokota; Barat S Venkataramany; Wladek Minor
Journal:  Protein Sci       Date:  2019-10-25       Impact factor: 6.725

Review 8.  The young person's guide to the PDB.

Authors:  Wladek Minor; Zbigniew Dauter; Mariusz Jaskolski
Journal:  Postepy Biochem       Date:  2016

Review 9.  Detect, correct, retract: How to manage incorrect structural models.

Authors:  Alexander Wlodawer; Zbigniew Dauter; Przemyslaw J Porebski; Wladek Minor; Robyn Stanfield; Mariusz Jaskolski; Edwin Pozharski; Christian X Weichenberger; Bernhard Rupp
Journal:  FEBS J       Date:  2017-11-27       Impact factor: 5.542

10.  Correcting the record of structural publications requires joint effort of the community and journal editors.

Authors:  Bernhard Rupp; Alexander Wlodawer; Wladek Minor; John R Helliwell; Mariusz Jaskolski
Journal:  FEBS J       Date:  2016-06-10       Impact factor: 5.542

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