Practical Guide to Homology Modeling: Difference between revisions

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 '''Gaps''' in the sequence alignment make errors in the model. Gaps are opened in a sequence alignment in order to optimize the alignment. Such gaps may be regarded as insertions or deletions, but since it is usually unclear which, these are commonly called by the noncommittal term ''indels''. The presence of large numbers of gapped residues in a sequence alignment guarantees that there will be errors in the homology model: missing residues, or residues in incorrect positions.
-:A '''gap in the template sequence''' means that the corresponding portion of the query is untemplated. Different homology modeling servers handle this differently. Swiss-Model includes the untemplated query residues, putting them in a loop (which may extend some distance away from the remainder of the domain when the loop is long).
+:A '''gap in the template sequence''' means that the corresponding portion of the query is untemplated. Different [[homology modeling servers]] handle this differently. Swiss-Model includes the untemplated query residues, putting them in a loop (which may extend some distance away from the remainder of the domain when the loop is long).
 :A '''gap in the query sequence''' means that the two residues flanking the gap will usually be peptide-bonded in the 3D model, yet the aligned template residues may not be close to each other.