Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration
By Saulius Grazulis, Adriana Daskevic, Andrius Merkys, Daniel Chateigner, Luca Lutterotti, Miguel Quirós, N. Serebryanaya, Peter Moeck, Robert T. Downs, Armel Le Bail. Nucleic Acids Res., 2011
1,169 citations recorded by the source corpus.
Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.
Subfields: Information Systems, Information Systems and Management, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/fd8ba9431c2a1780e27b6f5e1e4947db9c85801c
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In Information Systems and Management
In Molecular Biology
- G. Murshudov
- P. Emsley
- R. Nicholls
- F. Long
- G. Sheldrick
- Berend Smit
- Saulius Grazulis
- Antanas Vaitkus
Citations in the corpus
- Materials Cloud, a platform for open computational science (2020, methodology): “production-grade workflows. Users can import data into the platform either by uploading from their computer, or by importing data from connected open databases such as the Crystallography Open Database[27]oranydatabaseimplementingtheOPTIMADEstandard(optimade.org), includingAFLOW(aflow.org [9]), COD(cr”
- AceDRG: a stereochemical description generator for ligands (2017, background): “The number of such atom classes derived from the COD is around 260 000.”
- Limestone Calcination Nearby Equilibrium: Kinetics, CaO Crystal Structure, Sintering and Reactivity (2015, background): “389) available 246 from the Crystallography Open Database (COD) [37].”
- Crystal structure refinement with SHELXL (2015, methodology): “A simple solution would be for journals to require a confirmation that the full data have been deposited with the CSD (Bruno & Groom, 2014) or COD (Gražulis et al., 2012), analogous to the way in which the PDB requires deposition of the structural and reflection data before issuing a PDB ID. 2.3.”