Practical Guide to Homology Modeling: Difference between revisions
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: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 | :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. | ||
Templates determined by crystallography often have '''missing residues'''. [[FirstGlance in Jmol]] reports missing residues and marks their locations clearly. Missing residues have no coordinates in the crystallographic model due to disorder of those residues in the crystal. Thus, even though the sequences may align, some residues are absent in the 3D template, and it is unclear where to position those residues. Some [[homology modeling servers]] omit such residues entirely, producing an incomplete homology model. | Templates determined by crystallography often have '''missing residues'''. [[FirstGlance in Jmol]] reports missing residues and marks their locations clearly. Missing residues have no coordinates in the crystallographic model due to disorder of those residues in the crystal. Thus, even though the sequences may align, some residues are absent in the 3D template, and it is unclear where to position those residues. Some [[homology modeling servers]] omit such residues entirely, producing an incomplete homology model. | ||
