Theoretical models: Difference between revisions
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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.) | 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.) | ||
The success of fold prediction methods is assessed biannually in the ''Critical Assessment of Techniques for Protein Structure Prediction'' (CASP) competitions<ref>[http://predictioncenter.gc.ucdavis.edu/ Critical Assessment of Techniques for Protein Structure Prediction (CASP)].</ref>. Crystallographers submit sequences which they have solved, but for which the structures have not yet been published. Modelers predict the folds which are then compared with subsequently published structures. | The success of fold prediction methods is assessed biannually in the ''Critical Assessment of Techniques for Protein Structure Prediction'' (CASP) competitions<ref>[http://predictioncenter.gc.ucdavis.edu/ Critical Assessment of Techniques for Protein Structure Prediction (CASP)].</ref>. Crystallographers submit sequences which they have solved, but for which the structures have not yet been published. Modelers predict the folds which are then compared with subsequently published structures. Beginning in CASP5 (2002), the ability to predict [[Intrinsically Disordered Protein|intrinsic disorder]] was included<ref>PMID: 19774619</ref>. There are also competitions to predict protein-protein docking interactions<ref>[http://www.ebi.ac.uk/msd-srv/capri/ CAPRI: Critical Assessment of PRediction of Interactions].</ref> | ||
==See Also== | ==See Also== | ||
