Homology modeling servers
From Proteopedia
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| + | ==Problems== | ||
| + | ===Sequence Numbering Anomalies=== | ||
| + | It is common for the sequences of proteins in [[PDB]] structures to begin with a number other than 1. Discontinuities in sequential numbering also occur. | ||
| + | * '''Phyre2''': In early April, 2011, Phyre2 numbered the aligned portion of the template sequence incorrectly when the above kinds of sequence anomalies occur in the template [[PDB]] file. The development team has acknowledged the problem and is working on a fix. | ||
==See Also== | ==See Also== | ||
Revision as of 16:30, 21 April 2011
There are a number of free servers that create homology models (also called comparative models) for a submitted amino acid sequence, or that offer libraries of 3D models created in advance for protein sequences. The performance of homology modeling methods is evaluated in an international, biannual competition called CASP. A comparison of 10 servers is included in the 2009 description of Phyre by Kelley and Sternberg[1], which also offers guidance in how to use these servers effectively.
The list below is incomplete, and may not include some of the best servers, nor does it include assessments of server performance.
- 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.
- ModBase: Database of Comparative Protein Structure Models allows users to calculate comparative models on demand.
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Handling of gaps
There are three kinds of gaps that present challenges when creating a homology model. It is important to know how a given server handles these challenges.
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Server |
Sequence Alignment[2] |
Template residues lacking 3D coordinates |
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Untemplated |
Gap in Target |
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Swiss-Model (Automated Mode) |
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Problems
Sequence Numbering Anomalies
It is common for the sequences of proteins in PDB structures to begin with a number other than 1. Discontinuities in sequential numbering also occur.
- Phyre2: In early April, 2011, Phyre2 numbered the aligned portion of the template sequence incorrectly when the above kinds of sequence anomalies occur in the template PDB file. The development team has acknowledged the problem and is working on a fix.
See Also
- Homology modeling at Wikipedia.
- User:Wayne Decatur/Homology Modeling
References and Notes
- ↑ Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 2009;4(3):363-71. PMID:19247286 doi:10.1038/nprot.2009.2
- ↑ Alignment between the target and template sequences. See Homology modeling.
