How to predict structures with AlphaFold: Difference between revisions
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[[FirstGlance in Jmol]] version 3.7 (when released) will automatically color uploaded AlphaFold models by estimated reliability per residue ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). | [[FirstGlance in Jmol]] version 3.7 (when released) will automatically color uploaded AlphaFold models by estimated reliability per residue ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). | ||
===Intrinsic Disorder=== | |||
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. | ||
===Relative Positions of Domains=== | |||
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]. | 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]. | ||
===Recycles For Convergence=== | |||
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. | ||
