Practical Guide to Homology Modeling: Difference between revisions
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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. | ||
===Sidechain rotamer positions will be incorrect=== | |||
Even when the sequence alignment and template result in a correct backbone fold for the homology model, the sidechain rotamer positions will be incorrect. Despite knowing where each alpha carbon atom is located, theory does not correctly predict how the sidechains will fit together. At best, the sidechain rotamer positions will avoid steric clashes and electrostatic repulsions of like charges, and may optimize some salt bridges and hydrogen bonds. However, when a high quality empirical model becomes available, the details of sidechain packing in the homology model will be shown to be incorrect. | |||
== References == | == References == | ||
<references/> | <references/> | ||
