Homology modeling servers: Difference between revisions

''The list below is incomplete, and may not include some of the best servers, nor does it include assessments of server performance.''

* [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.

Sequence Alignment<ref>Alignment between the target and template sequences. See [[Homology modeling]].</ref>

Untemplated Target Residues<br>(Gap in Template Sequence)

Gap in Target Sequence

Untemplated target residues (aligned with a gap in the template sequence) are present in the 3D model, and are indicated with a high [[temperature value]]. This appears to be true regardless of the length of the untemplated region. Long untemplated regions may occur in the 3D model as a long hairpin loop extending away from a compact domain, making their lack of template fairly obvious.

Omitted in the sequence alignment, yet not indicated there by a gap. The 3D model lacks a spatial gap between the residues at the gap boundries, effectively ligating** them . This causes a shift in target-template registration, and produces a 3D model that fails to make apparent the absence of some residues in the template.*

For short untemplated regions (e.g. 1-5 untemplated residues), the untemplated target residues are present in the 3D model, and registration is maintained according to the sequence alignment by bunching up the untemplated residues in the 3D model, allowing the untemplated target residues to bulge away from the template in the 3D model.

<font color="red">Caution:</font> For long untemplated regions (e.g. 87 residues), the untemplated target residues are omitted from the 3D model, effectively ligating** the templated boundary residues together. The omission fails to reveal, in the 3D model, that a large untemplated region exists.

<font color="red">Caution:</font> Due to errors in the sequence alignment (missing segments of the target sequence and numbering errors, see below), analysis of Phyre2's behavior has been postponed, pending correction of these errors.

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]]).