Text Box: Iowa State University Text Box: DEPARTMENT OF MATHEMATICS

The geometric dimensions of proteins: bond lengths, bond angles, and torsion angles, as can be observed at the atomic level.

With Andrew severin, Xiaoyong Huang, Mgavi Brathwaite, di wu, ...

Proteins fold to unique 3D structures to function. Structures are crucial for the understanding of the proteins’ biological functions. The structures can be viewed at different levels: atoms, residues, secondary structures, domains, or the entire protein, where there are different geometric forms and can be characterized with different geometric measures: distances between atoms or residues, triangles formed by adjacent three atoms, tetrahedrons formed by adjacent four atoms, the volumes of the residues, the shapes of the secondary structures, the orientations of the side chains, and the areas of the protein surfaces, etc. These geometric properties of proteins have not been well studied, but they are important for analysis, classifications, as well as predictions of protein structures.

Text Box: Protein Geometry databases Text Box: Proteins do share many common geometric properties. For example, the bond lengths and bond angles of same types do not vary much from protein to protein, and inter-atomic distances and dihedral angles of same types have non-uniform distributions in databases of known protein structures. We are interested in developing a group of protein geometry databases, each can be used for storing and querying the distributions of a specific geometric property of protein under various conditions. In the protein inter-atomic distance distributions database (PIDD) developed by Di Wu, Feng Cui, et al., for example, the distances are classified with their associated atoms, residues, sequence separations, etc., and the distributions of the distances are then profiled and can be queried at any time.

Phone: 515-294-8165

Fax: 515-294-5454

E-mail: zhijun@iastate.edu

Contact information:
Text Box: Different types of inter-atomic distances have different distributions in databases of known protein structures. Text Box: See PIDD for more ...