Related Experiment Videos
Protein superfamily members as targets for computer modeling: the carbohydrate recognition domain of a macrophage
R E Stenkamp1, A Aruffo, J Bajorath
1Department of Biological Structure, University of Washington, Seattle 98195, USA. stenkamp@u.washington.edu
Abstract:
Members of protein superfamilies display similar folds, but share only limited sequence identity, often 25% or less. Thus, it is not straightforward to apply standard homology modeling methods to construct reliable three-dimensional models of such proteins. A three-dimensional model of the carbohydrate recognition domain of the rat macrophage lectin, a member of the calcium-dependent (C-type) lectin superfamily, has been generated to illustrate how information provided by comparison of X-ray structures and sequence-structure alignments can aid in comparative modeling when primary sequence similarities are low.