DaRa - DAtabase for RApid search of structural neighbours for proteins based on their SAXS patterns

On-line summary and downloadable file content for main DaRa service

DaRa returns results in two ways: first is on–line summary displayed after DaRa finishes its work and the second is compressed file.

Please note: both sets are not completely identical. Compessed file contains all data showed on-line except information about proteins' secondary structure.

On–line summary is:
information about input data (name of file, number of structures selected for analysis as well the range of their molecular weights)
and
table(s) with names and secondary structure composition (alpha and beta elements procentage) of ten (or less) closest structural homologs for low angle part of scattering data, for medium angle part (if s_max is less then 0.75 Å) and for full range of angles (if s_max is less then 0.4 Å).

Secondary structure analysis is pre–done for all protein structures and stored. Method to recognize secondary structural elements in proteins is automatic algorithm Stride for secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information.

References

Stride web–page

D. Frishman, P. Argos (1995) Knowledge-Based Protein Secondary Structure Assignment Proteins: Structure, Function and Genetics, 23 p. 566

M. Heinig, D. Frishman (2004) STRIDE: a Web server for secondary structure assignment from known atomic coordinates of proteins Nucl. Acids Res., 32, W500–2

Compressed file "results.tar.gz" contains:

*_int.dat	experimental smoothed intensity cutted from input GNOM file;
full_list.lst	the full list of proteins, i.e. the section of the database to be screened;
sort_rf_i.log	list of intensities from proteins with similar overall shapes and corresponding values of Rf_i;
rf_i.fit	fits in the internal interval between the experimental data and ten the most close database patterns;
sort_rf_m.log	the same as sort_rf_i.log for proteins with similar domain architecture and corresponding values of Rf_m;
rf_m.fit	the same as rf_i.fit for medium inteval of scattering angles;
sort_rf_t.log	the same as sort_rf_i.log and sort_rf_m.log for proteins with similar overall structure and corresponding values of Rf_m;
rf_t.fit	the same as rf_i.fit and rf_m.fit for total inteval of scattering angles;
*.pdb.gz	protein structure similar either on overall shape or in domain architecture or similar based on full length scattering pattern comparison.

Files AAA*.int, AAA.pdb.gz with same first three letters in their names are corresponding to same structure.

Lite DaRa output:

information about input data (name of file, number of structures selected for analysis as well the range of their molecular weights)
and
table with names and secondary structure composition (alpha and beta elements procentage) of ten (or less) closest structural homologs for full available range of scatterig angles; please note that pdb files are downloadable.

On-line output for search of similar structures in terms of NSD:

table of pdb names and corresponded values of Normal Spacial Distribution.

To display files like *.int or *.fit you can download program sasplot (executable file "sasplot.exe", last version 03/05/2007 compressed into "sasplot.zip", ~210 kb).

Last update: 19/04/2009