The database BIOSCAT: a tool for structure research by scattering and hydrodynamic methods

The crystal structures of a large number of proteins and nucleic acids are known and the corresponding sets of coordinates are stored in the Brookhaven Protein Data Bank. For structure investigations of biological macromolecules in solution, scattering and hydrodynamical methods are powerful biophysical tools when starting the data interpretation on the basis of the crystal structure of the molecules. The database BIOSCAT covers the main structural parameters estimable by X-ray scattering, translation and rotation diffusion methods and the X-ray scattering intensities and low- and high-resolution real-space electron distance distribution functions of 70 biological macromolecules and of oligonucleotides in standard conformation. The parameters and the scattered intensities are calculated from the atomic coordinates using the improved cube method and the real-space functions are estimated via a termination-error-reduced Fourier sine transformation. The database access is organized by the program PASSDB, which can generally be used for `readable' databases. A simple query language allows enquiries into the database without knowledge of a programming language. The program CONVSQL converts the database into normalized relations that can be handled by structured query languages (SQLs).