Literature DB >> 19153462

The Biomolecular Crystallization Database Version 4: expanded content and new features.

Michael Tung1, D Travis Gallagher.   

Abstract

The Biological Macromolecular Crystallization Database (BMCD) has been a publicly available resource since 1988, providing a curated archive of information on crystal growth for proteins and other biological macromolecules. The BMCD content has recently been expanded to include 14 372 crystal entries. The resource continues to be freely available at http://xpdb.nist.gov:8060/BMCD4. In addition, the software has been adapted to support the Java-based Lucene query language, enabling detailed searching over specific parameters, and explicit search of parameter ranges is offered for five numeric variables. Extensive tools have been developed for import and handling of data from the RCSB Protein Data Bank. The updated BMCD is called version 4.02 or BMCD4. BMCD4 entries have been expanded to include macromolecule sequence, enabling more elaborate analysis of relations among protein properties, crystal-growth conditions and the geometric and diffraction properties of the crystals. The BMCD version 4.02 contains greatly expanded content and enhanced search capabilities to facilitate scientific analysis and design of crystal-growth strategies.

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Year:  2008        PMID: 19153462     DOI: 10.1107/S0907444908035440

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


  14 in total

1.  Protein flexibility: coordinate uncertainties and interpretation of structural differences.

Authors:  Alexander A Rashin; Abraham H L Rashin; Robert L Jernigan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-10-22

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.  Structure of the recombinant BPTI/Kunitz-type inhibitor rShPI-1A from the marine invertebrate Stichodactyla helianthus.

Authors:  Rossana García-Fernández; Tirso Pons; Arne Meyer; Markus Perbandt; Yamile González-González; Dayrom Gil; María de los Angeles Chávez; Christian Betzel; Lars Redecke
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-10-26

5.  Crystallization of Pseudomonas aeruginosa AmrZ protein: development of a comprehensive method for obtaining and optimization of protein-DNA crystals.

Authors:  Edward E Pryor; Daniel J Wozniak; Thomas Hollis
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-07-31

6.  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 7.  Computational crystallization.

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

Review 8.  The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability.

Authors:  Zygmunt S Derewenda; Adam Godzik
Journal:  Methods Mol Biol       Date:  2017

9.  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

10.  Correlation between protein sequence similarity and crystallization reagents in the biological macromolecule crystallization database.

Authors:  Hui-Meng Lu; Da-Chuan Yin; Yong-Ming Liu; Wei-Hong Guo; Ren-Bin Zhou
Journal:  Int J Mol Sci       Date:  2012-07-27       Impact factor: 6.208

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