To predict tertiary structure

-Use sequence analysis and low resolution spectroscopy (like circular dichroism and polarized IR) to predict a protein's secondary structural elements

-Can now use surface analysis to predict how these secondary structural elements will pack with each other

• Ridges should come into grooves in interacting faces
• Helix-helix interactions
  • Based on the surfaces of alpha-helices, we may expect that they pack together only in a few different ways

Chothia, C., Levitt, M. and Richardson, D. 1981. Helix to Helix Packing in Proteins. J. Mol. Biol. 145:215-250

Programs for exploring and evaluating various tertiary structures, given secondary structure

• ESCHER

Ausiello, G., Cesareni, G., and Helmer-Critterich, M. 1997. Proteins: Structure, Function, and Genetics. 28:556-567

CHI

Adams, P., Arkin, I., Engelman, D., Brünger, A. 1995. Nature Structural Biology. 2:154-162