Theoretical models: Difference between revisions
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==Ab Initio Models== | ==Ab Initio Models== | ||
When there is no template with sufficient sequence identity to use for homology modeling, one can use ''ab initio'' or ''de novo'' folding theory to | When there is no template with sufficient sequence identity to use for homology modeling, one can use ''ab initio'' or ''de novo'' folding theory to predict the structure of a target protein sequence. Such theory is about 70% successful at predicting [[secondary structure]]<ref>[http://cmgm.stanford.edu/WWW/www_predict.html Accuracy of Protein Structure Prediction] at Stanford University.</ref>. Tertiary structure prediction has modest success for small protein chains (80 amino acids or less), but is generally unable to predict the fold for longer chains. In about one out of four cases of small domains of less than 85 amino acids, the best predictions are within about 1.5 Å (RMS for carbon alphas) of the true structure<ref>PMID: 16166519</ref>. (Independent determinations of the same protein by empirical methods generally agree within about 0.5 Å RMS for carbon alphas.) | ||
