Homology Modeling - Utility

Utility

Uses of the structural models include protein–protein interaction prediction, protein–protein docking, molecular docking, and functional annotation of genes identified in an organism's genome. Even low-accuracy homology models can be useful for these purposes, because their inaccuracies tend to be located in the loops on the protein surface, which are normally more variable even between closely related proteins. The functional regions of the protein, especially its active site, tend to be more highly conserved and thus more accurately modeled.

Homology models can also be used to identify subtle differences between related proteins that have not all been solved structurally. For example, the method was used to identify cation binding sites on the Na+/K+ ATPase and to propose hypotheses about different ATPases' binding affinity. Used in conjunction with molecular dynamics simulations, homology models can also generate hypotheses about the kinetics and dynamics of a protein, as in studies of the ion selectivity of a potassium channel. Large-scale automated modeling of all identified protein-coding regions in a genome has been attempted for the yeast Saccharomyces cerevisiae, resulting in nearly 1000 quality models for proteins whose structures had not yet been determined at the time of the study, and identifying novel relationships between 236 yeast proteins and other previously solved structures.