How to predict structures with AlphaFold: Difference between revisions
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Each residue has an estimated reliability of its position (0-100) in the PDB [[temperature]] column. BEWARE that high values mean high confidence, and low values mean low confidence. This is the INVERSE of [[temperature|crystallographic temperature values]], where low values are good and high values are bad. | Each residue has an estimated reliability of its position (0-100) in the PDB [[temperature]] column. BEWARE that high values mean high confidence, and low values mean low confidence. This is the INVERSE of [[temperature|crystallographic temperature values]], where low values are good and high values are bad. | ||
===Visualization=== | |||
[[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}}'''). Version 3.6 can do this for AlphaFold Database PDB files (because they have a recognizable header section): click ''Reliability Estimates'' in the ''Views'' tab. | [[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}}'''). Version 3.6 can do this for AlphaFold Database PDB files (because they have a recognizable header section): click ''Reliability Estimates'' in the ''Views'' tab. | ||
After uploading your predicted model to [http://firstglance.jmol.org FirstGlance.Jmol.Org], you can visualize | |||
* Secondary structure (Views tab) | |||
* Distribution of hydrophobic vs. polar residues (Views tab: integral membrane proteins will have large hydrophobic surfaces while soluble proteins will have hydrophobic cores revealed by the ''Slab'' button) | |||
* Distribution of charges (Views tab: nucleic acid binding sites will have clusters of positive charges) | |||
* Disulfide bonds (Tools tab) | |||
===Intrinsic Disorder=== | ===Intrinsic Disorder=== | ||
