How to predict structures with AlphaFold: Difference between revisions
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Some models have high confidence in a folded [[domain]], and low confidence in a segment that is not part of a compact domain. Low-confidence segments may be [[Intrinsically_Disordered_Protein|intrinsically disordered]]. It is useful to compare [[Intrinsically_Disordered_Protein#Protein_disorder_predictors|predictions of disorder]] with AlphaFold reliability estimates. | Some models have high confidence in a folded [[domain]], and low confidence in a segment that is not part of a compact domain. Low-confidence segments may be [[Intrinsically_Disordered_Protein|intrinsically disordered]]. It is useful to compare [[Intrinsically_Disordered_Protein#Protein_disorder_predictors|predictions of disorder]] with AlphaFold reliability estimates. | ||
If the predicted model has more than one [[domain]], each domain may have high confidence, yet the relative positions of the domains may not. The estimated reliability of relative domain positions is in graphs of '''predicted aligned error''' (PAE) which are included in the downloadable zip file of results. For an explanation, see ''How should I interpret the relative positions of domains?'' in the [https://alphafold.ebi.ac.uk/faq AlphaFold Database FAQ]. | |||
You may be interested to note the number of recycles required for each model to converge to the specified tolerance. These numbers are not captured in the downloaded zip file. | You may be interested to note the number of recycles required for each model to converge to the specified tolerance. These numbers are not captured in the downloaded zip file. | ||
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</pre> | </pre> | ||
Notice that the model predicted 2nd had the best estimated reliability (pLDDT), and that the model ranked 3rd did not quite achieve the specified tolerance of 0.5 Å RMSD after 12 recycles. (12 was specified as the maximum in this job.) | Notice that the model predicted 2nd had the best estimated reliability (pLDDT), and that the model ranked 3rd did not quite achieve the specified tolerance of 0.5 Å RMSD after 12 recycles. (12 was specified as the maximum in this job.) | ||
Also notice that, in this case, all 3 models have low confidence (pLDDT < 70), and are of questionable value. | |||
==Downloading Results== | ==Downloading Results== | ||
