How to predict structures with AlphaFold: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 27: | Line 27: | ||
==Visualizing Predicted Structures== | ==Visualizing Predicted Structures== | ||
====Visualization==== | |||
[http://firstglance.jmol.org FirstGlance in Jmol] automatically colors its initial view of uploaded AlphaFold or RoseTTAFold 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. | |||
[http://firstglance.jmol.org/where.htm#uploading Upload] your predicted PDB file to [http://firstglance.jmol.org FirstGlance.Jmol.Org], which has many [http://firstglance.jmol.org/whatis.htm#unique unique conveniences and capabilities]. | |||
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]]) | |||
==Instructions for ColabFold== | ==Instructions for ColabFold== | ||
