  The tertiary structure of protein, as well as the local secondary structure
organization are fully determined by the angles of the peptidic bound. The
backbone dihedral angles not only determine the global fold of the protein, but
also the details of the local chain organization. Although a wealth of
structural information is available in different databases and numerous
structural biology softwares have been developed, rapid conformational
characterization remains challenging.
  We present here RamaDA, a program able to give a synthetic description of the
conformation of a protein. The RamaDA program is based on a model where the
Ramachadran plot is decomposed into seven conformational domains. Within the
framework of this model, each amino-acid of a given protein is assigned to one
of these domains.
  From this assignment secondary structure elements can be detected with an
accuracy equivalent to that of the DSSP program for helices and extended
strands, and with the added capability of detecting PolyProline II secondary
structures. Additionally, the determination of a z-score for each amino-acid of
the protein emphasizes any irregularities in the element.
  It is also possible to use this analysis to detect characteristic
conformational patterns. In the case of EF-hands, calcium-binding
helix-loop-helix domains, it is possible to design a strict consensus for the 9
amino-acids of the loop. 523 calcium binding protein files can be found into
the entire PDB with this pattern and only 2.7% false positive hits are
detected.
  The program RamaDA gathers several tools in one and is then able to give a
complete information on a protein structure, including loops and random coil
regions. Through the example of EF-hands, a promising approach of structural
biology is developed. RamaDA is freely available for download as well as online
usage at http://ramada.u-strasbg.fr
