Theoretical models: Difference between revisions

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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.


[http://swissmodel.expasy.org/ SWISS-MODEL] provides a free, fully-automated homology modeling service. Using the ''Automated Mode'', you submit a protein sequence. When the [[PDB]] contains an empirically-determined structure with sufficient sequence identity with your target sequence, it will be used as a template. The resulting homology model will be constructed automatically.
A number of free servers have libraries of homology models generated in advance for protein sequences, and many will create homology models for a submitted protein sequence. For more, please see
 
<blockquote>
[[Homology modeling servers]].
</blockquote>
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.
[http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase: Database of Comparative Protein Structure Models] also allows users to calculate comparative models on demand.


See also the list of resources at [[User:Wayne Decatur/Homology Modeling]].
See also the list of resources at [[User:Wayne Decatur/Homology Modeling]].
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