Homology modeling servers: Difference between revisions
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<center><table style="background:#ffff80;"><tr><td>CAUTION: Issues with servers, reported in this article, have not been updated since 2011.</td></tr></table></center> | |||
There are a number of free servers that create [[Theoretical_models#Homology_Models|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<ref>PMID: 19247286</ref>, which also offers guidance in how to use these servers effectively. | There are a number of free servers that create [[Theoretical_models#Homology_Models|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<ref>PMID: 19247286</ref>, which also offers guidance in how to use these servers effectively. | ||
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MetaServers are servers that submit your modeling job to other servers. | MetaServers are servers that submit your modeling job to other servers. | ||
* [http://www.proteinmodelportal.org/ Protein Model Portal (PMP)] a service of the Protein Structure Initiative. | * [http://www.proteinmodelportal.org/ Protein Model Portal (PMP)]<ref>PMID: 19037750</ref> a service of the Protein Structure Initiative. | ||
==Handling of gaps== | ==Handling of gaps== | ||
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==Problems== | ==Problems== | ||
===Sequence Numbering Anomalies=== | ===Sequence Numbering Anomalies=== | ||
It is common for the sequences of proteins in [[PDB]] structures to begin with a number other than 1 ([[2fsr]]:A, [[1ucy]]:E, [[1nsa]]), and to include a residue numbered zero ([[1avq]]:A, [[1bxw]]:A). Discontinuities in sequential numbering may occur ([[1igt]]:B, [[2fsr]]:A, [[1nsa]], [[1iao]]:B). Residues in the same chain may have the same sequence number, notably in the case of "insertions" relative to a reference sequence ([[1igt]]:B, [[1ucy]]). These inserted residues may all have the same number, but are distinguished by insertion codes, typically letters in alphabetical order. However, in rare cases, the letters may not be in alphabetical order, e.g. chain J in [[1ucy]]. An overview of sequence numbering anomalies in the [[PDB]], including further examples, is at [http://firstglance.jmol.org/seqspecs.htm Specification for Interactive Sequence Listings] (in [[FirstGlance in Jmol]]). | It is common for the sequences of proteins in [[PDB]] structures to begin with a number other than 1 ([[2fsr]]:A, [[1ucy]]:E, [[1nsa]]), and to include a residue numbered zero ([[1avq]]:A, [[1bxw]]:A). Discontinuities in sequential numbering may occur ([[1igt]]:B, [[2fsr]]:A, [[1nsa]], [[1iao]]:B). Residues in the same chain may have the same sequence number, notably in the case of "insertions" relative to a reference sequence ([[1igt]]:B, [[1ucy]]). These inserted residues may all have the same number, but are distinguished by insertion codes, typically letters in alphabetical order. However, in rare cases, the letters may not be in alphabetical order, e.g. chain J in [[1ucy]]. An overview of sequence numbering anomalies in the [[PDB]], including further examples, is at [[Unusual sequence numbering]]<!--[http://firstglance.jmol.org/seqspecs.htm Specification for Interactive Sequence Listings] (in [[FirstGlance in Jmol]])-->. | ||
* '''Phyre2''' - <font color="red">Caution</font>: 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. | * '''Phyre2''' - <font color="red">Caution</font>: 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. | ||
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==See Also== | ==See Also== | ||
*[[Practical Guide to Homology Modeling]] | |||
*[[Homology modeling]] | *[[Homology modeling]] | ||
*[[Theoretical models]] | *[[Theoretical models]] | ||