Homology modeling servers: Difference between revisions
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<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> 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. | ||
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<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. | <font color="red">Caution:</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. | ||
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<nowiki>**</nowiki>Covalent peptide bonds between amino acids are not explicit in [[PDB files]], but all commonly used software places covalent bonds based on interatomic distances. Thus, when a spatial gap is omitted in the 3D model, the two residues abutting the gap are effectively ligated. | <nowiki>**</nowiki>Covalent peptide bonds between amino acids are not explicit in [[PDB files]], but all commonly used software places covalent bonds based on interatomic distances. Thus, when a spatial gap is omitted in the 3D model, the two residues abutting the gap are effectively ligated. | ||
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<nowiki>***</nowiki>In the case examined, segments of the target sequence were missing from the sequence alignment for no apparent reason. | |||
==Problems== | ==Problems== | ||
