EMBL c/o DESY
Biological Small Angle Scattering Group

DaRa

DAtabase for RApid search of structural neighbours for proteins
based on their X–ray small–angle scattering patterns

Sokolova A. V.^1,3, Volkov V. V.¹, Svergun D. I.^1,2

¹Small angle scattering laboratory, Institute of Crystallography RAS
Leninskij pr. 59, 119333, Moscow, Russia
²European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY
Notkestrasse 85, D-22603, Hamburg, Germany
³Bragg Institute, Australian Nuclear Science and Technology Organization
New Illawarra Road, Lucas Heights, 2234, Sydney, Australia

The main idea of DaRa

Let assume, that you have experimental scattering pattern from a protein with unknown structure. To restore the overall shape ab initio one can employ programs DAMMIN and/or GASBOR.
Alternatively, using DaRa one can rapidly search for structural neighbours among aproximately sevel thousands known protein structures.
To optimize the search, the experimental data has to be first processed by the program GNOM.
DaRa directly reads in the output file given by GNOM, and you only need to specify the molecular mass of the protein to define the section of the database to be screened.

To test DaRa you can download a test GNOM–output file (~91 KB) which contains scattering pattern from myoglobin (1duo.pdb) with MW = 17 kDa.

It is strongly recommended to read carefully descriptions of algorithm behind DaRa and output data content.

DaRa now offers three independent services:

• Classical version allowed to find structural neighbours in terms of overall shape and internal architecture. This service will return to you full set of found similar shapes as well as log files contains calculated values of R-factors, selection of homologous is based on.
• Lite version does the same job as main DaRa algorithm but does not split experimental pattern into two part. DaRa Lite calculates R-factors between real data and calculated sets taking into account full available range of scattering vectors. Lite version will not create compressed results file but will allow to have a look on selected pdb files on-line and save pdp files one by one if necessary.

Update, April 20th, 2010

Additional links to proteins' primary sequences are now generated for quick and convenient way to align choosen structures. Links transfer you to corresponding pages provided by Protein Data Bank. You can copy the sequences and use, for example, service EMBOSS provided by EBI-EMBL for structures alignment.

• As known, DaRa finds homologous in terms of geometrical characteristic called NSD (see description of program SupComb for relevant information). Obviously, Protein Data Bank archive contains a lot of similar structures. In order to create adequate storage for DaRa and be able to operate with representative set of structures we are cutting a number of homologous in DaRa. You can check how many homologous (if any) in terms of NSD has protein of your interest by using separate service.

Contact address

Last update: 20/04/2010

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