Literature DB >> 16301801

Tapping the Protein Data Bank for crystallization information.

Thomas S Peat1, Jon A Christopher, Janet Newman.   

Abstract

A database application has been developed for the collection of crystallographic information. This database (the BDP) has been populated with the information found in the Protein Data Bank (PDB). The tool has been used to store crystallization data parsed out of the PDB and these data may be used to extend the crystallization information found in the Biological Macromolecule Crystallization Database (BMCD) and could be used to refine crystallization methodology. A standard is proposed for describing a crystallization experiment that will ease future crystallization data collations and analyses.

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Year:  2005        PMID: 16301801     DOI: 10.1107/S0907444905033202

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  11 in total

1.  Crystallization reports are the backbone of Acta Cryst. F, but do they have any spine?

Authors:  Janet Newman; Denis R Burton; Sofia Caria; Sebastien Desbois; Christine L Gee; Vincent J Fazio; Marc Kvansakul; Bevan Marshall; Grant Mills; Viviane Richter; Shane A Seabrook; Mingbo Wu; Thomas S Peat
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-06-30

2.  Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments.

Authors:  Lesa R Offermann; John Z He; Nicholas J Mank; William T Booth; Maksymilian Chruszcz
Journal:  J Struct Funct Genomics       Date:  2014-01-23

3.  BLASTing away preconceptions in crystallization trials.

Authors:  Gabriel Jan Abrahams; Janet Newman
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2019-02-21       Impact factor: 1.056

4.  A drunken search in crystallization space.

Authors:  Vincent J Fazio; Thomas S Peat; Janet Newman
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2014-09-30       Impact factor: 1.056

Review 5.  Computational crystallization.

Authors:  Irem Altan; Patrick Charbonneau; Edward H Snell
Journal:  Arch Biochem Biophys       Date:  2016-01-11       Impact factor: 4.013

6.  Data management in the modern structural biology and biomedical research environment.

Authors:  Matthew D Zimmerman; Marek Grabowski; Marcin J Domagalski; Elizabeth M Maclean; Maksymilian Chruszcz; Wladek Minor
Journal:  Methods Mol Biol       Date:  2014

7.  On the need for an international effort to capture, share and use crystallization screening data.

Authors:  Janet Newman; Evan E Bolton; Jochen Müller-Dieckmann; Vincent J Fazio; D Travis Gallagher; David Lovell; Joseph R Luft; Thomas S Peat; David Ratcliffe; Roger A Sayle; Edward H Snell; Kerry Taylor; Pascal Vallotton; Sameer Velanker; Frank von Delft
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-02-15

8.  Proline/alanine-rich sequence (PAS) polypeptides as an alternative to PEG precipitants for protein crystallization.

Authors:  André Schiefner; Rebecca Walser; Michaela Gebauer; Arne Skerra
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2020-07-01       Impact factor: 1.056

Review 9.  Crystallization screening: the influence of history on current practice.

Authors:  Joseph R Luft; Janet Newman; Edward H Snell
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2014-06-27       Impact factor: 1.056

10.  Analysis of crystallization data in the Protein Data Bank.

Authors:  Jobie Kirkwood; David Hargreaves; Simon O'Keefe; Julie Wilson
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-09-23       Impact factor: 1.056

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