Theoretical models: Difference between revisions
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==Homology Models== | ==Homology Models== | ||
===Method & Limitations=== | |||
''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. | ''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|evolutionary conservation]]. | 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|evolutionary conservation]]. | ||
===Paucity of Templates=== | |||
Empirically-determined templates with adequate sequence identity are available for less than half of all protein sequences. One of the major goals of [[structural genomics]] is to increase the sequence diversity of the available empirically-determined structures that can be used as templates for homology modeling. | Empirically-determined templates with adequate sequence identity are available for less than half of all protein sequences. One of the major goals of [[structural genomics]] is to increase the sequence diversity of the available empirically-determined structures that can be used as templates for homology modeling. | ||
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When no suitable template exists, the [http://targetdb.pdb.org Structural Genomics Target Database] should be searched with your sequence. In some cases, a sequence-similar protein has already been crystallized and diffracted, but the model may not have been completed, or the completed model may not yet have been deposited in the [[PDB]]. In such cases, it may be worthwhile to contact the team that has made the most progress on a closely related sequence. | When no suitable template exists, the [http://targetdb.pdb.org Structural Genomics Target Database] should be searched with your sequence. In some cases, a sequence-similar protein has already been crystallized and diffracted, but the model may not have been completed, or the completed model may not yet have been deposited in the [[PDB]]. In such cases, it may be worthwhile to contact the team that has made the most progress on a closely related sequence. | ||
See | ===See Also=== | ||
* [[Homology modeling]] | * [[Homology modeling]] | ||
* The list of resources at [[User:Wayne Decatur/Homology Modeling]]. | * The list of resources at [[User:Wayne Decatur/Homology Modeling]]. | ||
