Practical Guide to Homology Modeling: Difference between revisions
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In contrast, the median molecular mass of [[asymmetric units]] determined by X-ray crystallography is 50 KD<ref name="mmm" />, and a few are very large, such as virus capsids (e.g. 4qyk, ~2 million Daltons; 4v99, 10 million Daltons) or ribosomes (e.g. 4w2i, 4.5 million Daltons). | In contrast, the median molecular mass of [[asymmetric units]] determined by X-ray crystallography is 50 KD<ref name="mmm" />, and a few are very large, such as virus capsids (e.g. 4qyk, ~2 million Daltons; 4v99, 10 million Daltons) or ribosomes (e.g. 4w2i, 4.5 million Daltons). | ||
===Errors and uncertainties in the sequence alignment produce errors in the homology model=== | |||
The quality of a homology model depends upon the quality of the alignment between the query and template sequences. When the sequence identity '''falls below 35%''', the chances increase for errors in the alignment. Errors in the sequence alignment result in errors in positioning the query residues on the template fold; that is, errors in the 3D model. | |||
'''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 aligned 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 awat 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 must 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. | |||
== References == | == References == | ||
<references/> | <references/> | ||
