Practical Guide to Homology Modeling: Difference between revisions
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===Sidechain rotamer positions will be incorrect=== | ===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. | Even when the sequence alignment and template result in a correct backbone fold for the homology model, the sidechain rotamer positions (orientations relative to the alpha carbon position) 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. | ||
==Strengths of Homology Models== | ==Strengths of Homology Models== | ||
