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2016 ; 72
(Pt 11
): 1181-1193
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A public database of macromolecular diffraction experiments
#MMPMID27841751
Grabowski M
; Langner KM
; Cymborowski M
; Porebski PJ
; Sroka P
; Zheng H
; Cooper DR
; Zimmerman MD
; Elsliger MA
; Burley SK
; Minor W
Acta Crystallogr D Struct Biol
2016[Nov]; 72
(Pt 11
): 1181-1193
PMID27841751
show ga
The low reproducibility of published experimental results in many scientific
disciplines has recently garnered negative attention in scientific journals and
the general media. Public transparency, including the availability of `raw'
experimental data, will help to address growing concerns regarding scientific
integrity. Macromolecular X-ray crystallography has led the way in requiring the
public dissemination of atomic coordinates and a wealth of experimental data,
making the field one of the most reproducible in the biological sciences.
However, there remains no mandate for public disclosure of the original
diffraction data. The Integrated Resource for Reproducibility in Macromolecular
Crystallography (IRRMC) has been developed to archive raw data from diffraction
experiments and, equally importantly, to provide related metadata. Currently, the
database of our resource contains data from 2920 macromolecular diffraction
experiments (5767 data sets), accounting for around 3% of all depositions in the
Protein Data Bank (PDB), with their corresponding partially curated metadata.
IRRMC utilizes distributed storage implemented using a federated architecture of
many independent storage servers, which provides both scalability and
sustainability. The resource, which is accessible via the web portal at
http://www.proteindiffraction.org, can be searched using various criteria. All
data are available for unrestricted access and download. The resource serves as a
proof of concept and demonstrates the feasibility of archiving raw diffraction
data and associated metadata from X-ray crystallographic studies of biological
macromolecules. The goal is to expand this resource and include data sets that
failed to yield X-ray structures in order to facilitate collaborative efforts
that will improve protein structure-determination methods and to ensure the
availability of `orphan' data left behind for various reasons by individual
investigators and/or extinct structural genomics projects.
free
free
free
