Practical Guide to Homology Modeling: Difference between revisions
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Given the limitations explained above, you might well wonder whether homology models have any uses. Provided that the sequence alignment is reliable (about 35% identity or more), and if the sequence alignment lacks numerous or large gaps (indels), the backbone fold is likely to be correct. This provides a great deal of information despite the inaccuracies in sidechain positions. | Given the limitations explained above, you might well wonder whether homology models have any uses. Provided that the sequence alignment is reliable (about 35% identity or more), and if the sequence alignment lacks numerous or large gaps (indels), the backbone fold is likely to be correct. This provides a great deal of information despite the inaccuracies in sidechain positions. | ||
*The model | *The model suggests which residues are on the '''surface''' and which are '''buried'''. | ||
*If mutagenesis studies have shown phenotypic changes, it will be useful to see where the crucial residues lie in the homology model. | *If mutagenesis studies have shown phenotypic changes, it will be useful to see where the crucial residues lie in the homology model. | ||