Biotechnologijos institutas yra  mokslini? tyrim? institucija, siekianti užtikrinti valstyb?s pažang? spar?iai besivystan?iose gyvyb?s moksl? ir biotechnologij? srityse, pl?toti tarptautinio lygio molekulin?s biotechnologijos tyrimus, skatinti tarpdisciplininius tyrimus bei mokslo ir verslo bendradarbiavim?

Crystallography Open Database COD

Spausdinti
The COD project (abbreviated from the "Crystallography Open Database", http://www.crystallography.net/) aims at collecting in a single open access database all organic, inorganic and metal organic structures [1] (except for the structures of biological macromolecules that are available at the PDB [2]). The database was founded by Armel Le Bail, Lachlan Cranswick, Michael Berndt, Luca Lutterotti and Robert M. Downs in February 2003 as a response to Michael Berndt’s letter published in the Structure Determination by Powder Diffractometry (SDPD) mailing list [3]. Since December 2007 the main database server is maintained and new software is developed in the Vilnius University Institute of Biotechnology by Saulius Gražulis and Andrius Merkys, and has now over 200 thousand records describing structures published in major crystallographic and chemical peer-reviewed journals [4]. Most of the mineral data is obtained from the AMCSD [5], donated by its maintainer and COD co-founder Robert M. Downs.

The database presents itself on the Internet as a Web site (Fig. 1a) with the basic data search and download capabilities, designed by Armel Le Bail and Michael Berndt. In addition, registered users may deposit new data into the database, either form the previous publications or as personal communications, using the deposition web site designed in the VU Institute of Biotechnology by Saulius Gražulis, Justas Butkus and Andrius Merkys. The deposition software performs rigorous checks of syntax and semantics, thus ensuring high quality of records deposited in the COD.

a)

b)

Fig. 1 a) Web site and search interface of the Crystallography Open Database (COD) permits searches of crystallographic data by a range of parameters and unrestricted retrieval of the found data. b) data can be viewed on-line in the JMol applet or downloaded for further processing, either record-wise or in bulk.

The retrieved COD records can be viewed on-line (Fig. 1b) or downloaded for further processing. For massive data mining, COD permits downloads and updates of the whole database using Subversion, Rsync or HTTP protocols. The ease of access to COD data has spurred the use of this resource for software testing [6], teaching [7], and research [8].

The open nature of the COD permitted numerous mirrors around the globe [9-12] and specifically tailored COD database variants [7]. At present, this is the most comprehensive open resource for small molecule structures, freely available to all scientists in Lithuania and worldwide.

References

1. Gražulis, S.; Chateigner, D.; Downs, R. T.; Yokochi, A. F. T.; Quirós, M.; Lutterotti, L.; Manakova, E.; Butkus, J.; Moeck, P. & Le Bail, A. (2009). Crystallography Open Database – an open-access collection of crystal structures, Journal of Applied Crystallography 42 : 726-729.

2. Berman, H.; Henrick, K. & Nakamura, H. (2003). Announcing the worldwide Protein Data Bank, Nat Struct Mol Biol 10 : 980-980.

3. Berndt, M. (2003). Open crystallographic database - a role for whom?, http://tech.groups.yahoo.com/group/sdpd/message/1016 (retrieved 2013.01.31).

4. Gražulis, S.; Daškevi?, A.; Merkys, A.; Chateigner, D.; Lutterotti, L.; Quirós, M.; Serebryanaya, N. R.; Moeck, P.; Downs, R. T. & Le Bail, A. (2012). Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration, Nucleic Acids Research 40 : D420-D427.

5. Rajan, H.; Uchida, H.; Bryan, D.; Swaminathan, R.; Downs, R. & Hall-Wallace, M. (2006). Building the American Mineralogist Crystal Structure Database: A recipe for construction of a small Internet database. In: Sinha, A. (Ed.), Geoinformatics: Data to Knowledge, Geological Society of America.

6. Grosse-Kunstleve, R. & Gildea, R. (2011). Computational Crystallography Initiative: COD stats, http://cci.lbl.gov/cod_stats/ (retrieved 2013.01.31).

7. Moeck, P. (2004). EDU-COD: Educational Subset of COD, http://nanocrystallography.research.pdx.edu/search/edu/ (retrieved 2013.01.31).

8. First, E. L. & Floudas, C. A. (2013). MOFomics: Computational pore characterization of metal–organic frameworks, Microporous and Mesoporous Materials 165 : 32-39.

9. Quirós-Olozábal, M. (2006). COD Mirror of Granada University, http://qiserver.ugr.es/cod/ (retrieved 2013.01.31).

10. Moeck, P. (2007). Crystallography Open Database Mirror, http://nanocrystallography.research.pdx.edu/search/codmirror/ (retrieved 2013.01.31).

11. Gražulis, S. (2007). COD Mirror in Vilnius, http://cod.ibt.lt/ (retrieved 2013.01.31).

12. Chateigner, D. (2010). Crystallography Open Database Mirror at ENSICAEN, http://cod.ensicaen.fr/ (retrieved 2013.01.31).