Practical Guide to Homology Modeling: Difference between revisions
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*If mutagenesis studies have shown phenotypic changes, it will be useful to see where the crucial residues lie in the homology model. | *If mutagenesis studies have shown phenotypic changes, it will be useful to see where the crucial residues lie in the homology model. | ||
*The distribution of evolutionarily conserved residues may suggest functional sites. For example, coloring the homology model by evolutionary conservation (e.g. with the [[ConSurf Server]]) may show '''patches or pockets of highly conserved residues'''. Pay attention to which residues may be missing from the homology model for the reasons explained above. Some missing residues could be highly conserved. | *The distribution of evolutionarily conserved residues may suggest functional sites. For example, coloring the homology model by evolutionary conservation (e.g. with the [[ConSurfDB_vs._ConSurf|ConSurf Server]]) may show '''patches or pockets of highly conserved residues'''. Pay attention to which residues may be missing from the homology model for the reasons explained above. Some missing residues could be highly conserved. | ||
The distribution of '''charges''' on the surface may be useful. For example, a large region or pocket with exclusively positive charges may be a binding site for nucleotides, DNA or RNA. A region devoid of charges suggests interaction with something hydrophobic<ref>Lipases commonly have a hydrophobic surface (devoid of charges) around their active sites. See [[Lipase lid morph]].</ref>Remember that the fine details of charge distribution will be incorrect; however the general arrangement may be informative. Also pay attention to whether some charged residues are missing in the model, as explained above, due to gaps in the sequence alignment or missing residues in the template. [[FirstGlance in Jmol]] quantitates missing charges. | *The distribution of '''charges''' on the surface may be useful. For example, a large region or pocket with exclusively positive charges may be a binding site for nucleotides, DNA or RNA. A region devoid of charges suggests interaction with something hydrophobic<ref>Lipases commonly have a hydrophobic surface (devoid of charges) around their active sites. See [[Lipase lid morph]].</ref>Remember that the fine details of charge distribution will be incorrect; however the general arrangement may be informative. Also pay attention to whether some charged residues are missing in the model, as explained above, due to gaps in the sequence alignment or missing residues in the template. [[FirstGlance in Jmol]] quantitates missing charges. | ||
== References == | == References == | ||
<references/> | <references/> | ||
