Homology modeling servers: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) No edit summary |
||
| (16 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
<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. | ||
| Line 4: | Line 6: | ||
<center><table style="background: #ffe0a0;" width="90%" cellpadding="6"> | <center><table style="background: #ffe0a0;" width="90%" cellpadding="6"> | ||
<tr> | <tr> | ||
<td><b>Terminology:</b> The sequence with unknown 3D structure is usually called the <b>target</b>. It is modeled on the <b>template</b>. Because those two terms are similar | <td><b>Terminology:</b> The sequence with unknown 3D structure is usually called the <b>target</b>. It is modeled on the <b>template</b>. Because those two terms are similar, sometimes leading to confusion, we shall call the target the <b>query</b>.</td> | ||
</tr></table></center> | </tr></table></center> | ||
''The list below is incomplete, and may not include some of the best servers, nor does it include assessments of server performance. Please help by adding additional servers.'' | ''The list below is incomplete, and may not include some of the best servers, nor does it include assessments of server performance. Please help by adding additional servers.'' | ||
| Line 11: | Line 13: | ||
* [http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase: Database of Comparative Protein Structure Models] allows users to calculate comparative models on demand. | * [http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase: Database of Comparative Protein Structure Models] allows users to calculate comparative models on demand. | ||
*[http://www.ncbi.nlm.nih.gov/pubmed/17640066 The Homology Modeling Automatically (HOMA) web site]. | |||
*[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ I-Tasser], formerly known as 'the Zhang lab-Server' - employs comparative protein modelling based on protein threading and has won the last few [[CASP]] events. | |||
*[http://www.yasara.org/ YASARA] - Yet Another Scientific Artificial Reality Application) features a complete homology modeling module that fully automatically takes all the steps from an amino acid sequence to a refined high-resolution model using a [[CASP]] approved protocol. | |||
===MetaServers=== | |||
MetaServers are servers that submit your modeling job to other servers. | |||
* [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== | ||
| Line 60: | Line 73: | ||
==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. | ||
| Line 68: | Line 81: | ||
==See Also== | ==See Also== | ||
*[[Practical Guide to Homology Modeling]] | |||
*[[Homology modeling]] | |||
*[[Theoretical models]] | |||
*[http://en.wikipedia.org/wiki/Homology_modeling Homology modeling] at Wikipedia. | *[http://en.wikipedia.org/wiki/Homology_modeling Homology modeling] at Wikipedia. | ||
*[[User:Wayne Decatur/Homology Modeling]] | *[[User:Wayne Decatur/Homology Modeling]] | ||
* An [http://www.jove.com/video/3259/a-protocol-for-computer-based-protein-structure-and-function-prediction article and video entitled "A Protocol for Computer-Based Protein Structure and Function Prediction"] at the [http://www.jove.com/ Journal of Visualized Experiments] illustrates and dicusses the use of the I-TASSER server for protein structure and function prediction. | |||
* [[Structural bioinformatics servers]] | |||
==References and Notes== | ==References and Notes== | ||
<references /> | <references /> | ||