Download "An Introduction to Modeling Structure from Sequence". In: Current

between overall fold and biochemical function is often quite loose, especially for some
protein superfamilies (Hegyi and Gerstein, 2001). Nevertheless, comparing a protein’s
fold with those already known is an important and sometimes powerful method. Liisa
Holm, whose program DALI (UNIT 5.5) is the most widely used tool for this purpose,
describes in her unit in this chapter how that tool should be employed. As the pace of
structure determination increases, DALI will be in the vanguard not only for comparison
of structures but also for assembling the database of fold libraries and assessing fold
divergence.
The growth of structure determination has turned most biochemists and biologists into
consumers of structural information. Genomics is accelerating this trend. As the demand
for such information continues to outstrip the supply, all aspects of structure modeling
assume increasing importance. For those who have yet to try their hand at such endeavors,
the encouraging news is that the tools are getting easier to use as well as more accurate.
Dip into the protocols in this chapter and see!
LITERATURE CITED
Hegyi, H. and Gerstein, M. 2001. Annotation transfer for genomics: Measuring functional divergence in
multi-domain proteins. Genome Res. 11:1632-1640.
Hou, J., Jun, S.R., Zhang, C., and Kim, S.H. 2005. Global mapping of the protein structure space and
application in structure-based inference of protein function. Proc. Natl. Acad. Sci. U.S.A. 102:36513656.
Kim, Y., Yakunin, A.F., Kuznetsova, E., Xu. X., Pennycooke, M., Gu, J., Cheung, F., Proudfoot, M.,
Arrowsmith, C.H., Joachimiak, A., Edwards, A.M., and Christendat, D. 2004. Structure- and functionbased characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum. J. Biol.
Chem. 279:517-526.
Sadreyev, R.I. and Grishin, N.V. 2006. Exploring dynamics of protein structure determination and homologybased prediction to estimate the number of superfamilies and folds. BMC Struct. Biol. 6:6.
Contributed by Gregory A. Petsko
Brandeis University
Waltham, Massachusetts
Modeling
Structure from
Sequence
5.1.3
Current Protocols in Bioinformatics
Supplement 15