Template:Homology Modeling Intro
Homology models, also called comparative models, are obtained by folding a target protein sequence to fit an empirically-determined template model. The registration between residues in the target and template is determined by an amino acid sequence alignment between the target and template sequences. Errors or uncertainties in the sequence alignment result in errors or uncertainties in the homology model. Portions of the target sequence cannot be modeled when there are Insertions/deletions in either sequence, or portions of the template that lack coordinates due to crystallographic disorder. Provided there is sufficient sequence identity between the target and template, the main chain in homology models is usually mostly correct. However, the positions of sidechains in homology models are usually incorrect.
Nevertheless, homology models are useful for seeing low-resolution features, such as which residues are on the surface or buried, which are close to other features of interest (such as a putative active site), and the overall distribution of charges and evolutionary conservation.
Attempts to improve homology models by molecular dynamics simulations have not been successful: "in most cases, simulations initiated from homology models drift away from the native structure"[1].
- ↑ Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins. 2012 Aug;80(8):2071-9. doi: 10.1002/prot.24098. Epub 2012 May 15. PMID:22513870 doi:10.1002/prot.24098
