Homology modeling servers: Difference between revisions

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.

The 3D model takes a shortcut, skipping the residues in the template aligned with the gap. This causes the 3D template to bulge away from the 3D target model in this region, and permits registration to be maintained.

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 (unless the structural alignment is examined as the downloadable ''Project'' in [[DeepView]]). The absence of some residues will affect analyses of the 3D model, such as charge distribution, and distribution of [[Evolutionary Conservation|evolutionary conservation]].

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 1:</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 2:</font> Due to errors in the sequence alignment (missing segments of the target sequence*** and numbering errors, see below), further analysis of Phyre2's behavior has been postponed, pending correction of these errors.