Homology Modeling: A Brief Summary
Abstract Homology models can help you figure out where the alpha carbons of key residues are in the folded protein. They can be used to direct mutagenesis experiments or to test hypotheses about structure-function relationships. Homology models are unreliable in predicting the conformations of insertions or deletions, that is, portions of the sequence that do not align with the template sequence, as well as sidechain position details. Unless the sequence identity with the template is greater than 70%, homology models are unlikely to be useful in modelling ligand docking (drug design), and even then, they are less reliable than an empirical crystallographic or NMR structure. Introduction Assume you want to know the 3D structure of a target protein that hasn't been solved empirically through X-ray crystallography or NMR. You only have the sequence. If an empirically determined 3D structure for a sufficiently similar protein is available (50% or better sequence identity is preferable)...