How to predict structures with AlphaFold: Difference between revisions

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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
30,118 edits
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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. Uploading your PDB file to [http://firstglance.jmol.org FirstGlance in Jmol] will automatically color each residue by its estimated reliability.
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. Uploading your PDB file to [http://firstglance.jmol.org FirstGlance in Jmol] will automatically color each residue by its estimated reliability.


====Visualization====


[[FirstGlance in Jmol]] automatically colors its initial view of uploaded AlphaFold models by estimated reliability per residue ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). After you go to other views or tools, you can always get back to this color scheme by clicking ''Reliability Estimates'' in the ''Views'' tab.
After uploading your predicted model to [http://firstglance.jmol.org FirstGlance.Jmol.Org], you can easily visualize
* Estimated reliability per residue
* 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)
* Domain structure and positions of the ends of the polypeptide chain (Views tab: N -> C Rainbow)
* Locations of functional sites by evolutionary conservation (see instructions at [[How_to_see_conserved_regions]])


====Intrinsic Disorder====
====Intrinsic Disorder====
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