Literature DB >> 27229767

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

Bernhard Rupp1,2, Alexander Wlodawer3, Wladek Minor4, John R Helliwell5, Mariusz Jaskolski6.   

Abstract

Seriously flawed and even fictional models of biomolecular crystal structures, although rare, still persist in the record of structural repositories and databases. The ensuing problems of database contamination and persistence of publications based on incorrect structure models must be effectively addressed. The burden cannot be simply left to the critical voices who take the effort to contribute dissenting comments that are mostly ignored. The entire structural biology community, and particularly the journal editors who exercise significant power in this respect, must engage in a constructive dialog lest structural biology lose its credibility as an evidence-based empirical science.
© 2016 Federation of European Biochemical Societies.

Entities:  

Keywords:  X-ray crystal structure models; biomolecular crystallography; database integrity; error correction; structural databases

Mesh:

Substances:

Year:  2016        PMID: 27229767      PMCID: PMC5124416          DOI: 10.1111/febs.13765

Source DB:  PubMed          Journal:  FEBS J        ISSN: 1742-464X            Impact factor:   5.542


  28 in total

1.  Questions about the structure of the botulinum neurotoxin B light chain in complex with a target peptide.

Authors:  B Rupp; B Segelke
Journal:  Nat Struct Biol       Date:  2001-08

2.  Cocrystal structure of synaptobrevin-II bound to botulinum neurotoxin type B at 2.0 A resolution.

Authors:  M A Hanson; R C Stevens
Journal:  Nat Struct Biol       Date:  2000-08

3.  Additional Comment on Three X-ray Crystal Structure Papers.

Authors:  Robyn Stanfield; Edwin Pozharski; Bernhard Rupp
Journal:  J Immunol       Date:  2016-01-15       Impact factor: 5.422

4.  Comment on Three X-ray Crystal Structure Papers.

Authors:  Robyn Stanfield; Edwin Pozharski; Bernhard Rupp
Journal:  J Immunol       Date:  2016-01-15       Impact factor: 5.422

5.  Real-space solution to the problem of full disclosure.

Authors:  Bernhard Rupp
Journal:  Nature       Date:  2006-12-14       Impact factor: 49.962

6.  Crystallography: crystallographic evidence for deviating C3b structure.

Authors:  Bert J C Janssen; Randy J Read; Axel T Brünger; Piet Gros
Journal:  Nature       Date:  2007-08-09       Impact factor: 49.962

7.  Structural evaluation of a mimicry-recognizing paratope: plasticity in antigen-antibody interactions manifests in molecular mimicry.

Authors:  Suman Tapryal; Vineet Gaur; Kanwal J Kaur; Dinakar M Salunke
Journal:  J Immunol       Date:  2013-06-03       Impact factor: 5.422

8.  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

9.  And the second shall be first.

Authors:  Gregory A Petsko
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

10.  Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.

Authors:  Maria A Schumacher; Nam K Tonthat; Jeehyun Lee; Fernando A Rodriguez-Castañeda; Naga Babu Chinnam; Anne K Kalliomaa-Sanford; Irene W Ng; Madhuri T Barge; Porsha L R Shaw; Daniela Barillà
Journal:  Science       Date:  2015-09-04       Impact factor: 47.728

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  21 in total

Review 1.  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

Review 2.  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

3.  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

4.  Online tools for enhancing presentation, understanding, and retention of 3D structural data.

Authors:  Alexander Wlodawer
Journal:  FEBS J       Date:  2017-12       Impact factor: 5.542

5.  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

6.  Perspectives and expectations in structural bioinformatics of metalloproteins.

Authors:  Sen Yao; Robert M Flight; Eric C Rouchka; Hunter N B Moseley
Journal:  Proteins       Date:  2017-03-15

7.  Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography.

Authors:  John R Helliwell
Journal:  Methods Mol Biol       Date:  2022

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

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

9.  Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies.

Authors:  John R Helliwell
Journal:  Acta Crystallogr A Found Adv       Date:  2021-05-04       Impact factor: 2.290

Review 10.  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

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