DaRa

The small angle X–ray scattering intensity I(s) from a dilute solution of macromolecules is an isotropic function of momentum transfer s = 4πsinθ/λ, where 2θ is the scattering angle, and λ is the X–ray wavelength.
A low angle part of a SAXS pattern in the range of s from 0 to about 0.15 Å^-1 (corresponding to resolution up to about 40 Å) provides information about the overall shape of the protein.
A medium angle part of the curve (range of s from about 0.4 to 0.9 Å^-1; resolution from 15 to 7 Å) contains information about the internal (tertiary and secondary)structure.
Next picture displays the internal and medium parts of scattering patterns (dashed and dotted lines, respectively).

patterns_resolution

The DaRa contains about seven thousands scattering patterns calculated by program CRYSOL from proteins with known atomic structure taken from archives of two wide known databases: Protein Data Bank (H. M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980) and Macromolecular Structure Database.
Taking SAXS experimental scattering pattern from an unknown protein pre-processed by program GNOM, DaRa selects proteins with close (±7%) molecular weights and finds the structures with similar overall shapes and domain architecture.

The main idea of the algorithm is:

agreement between the internal parts of small angle X–ray scattering patterns from two proteins means similarity of proteins overall shapes (next picture, left panel);
agreement between the closeness of medium parts of two small angle X–ray scattering curves indicates analogy in domain architecture of corresponding proteins (next picture, right panel).

similarities_1 similarities_2

For more information about algorithm used in our database you can download English and/or Russian versions of article about DaRa:

english version (PDF format ~615 kb)
russian version (MS WORD format ~1.2 Mb)

Last update: 19/04/2009