Resources: Finding the structure of a protein, or predicting it with AlphaFold, & electrostatic potential maps Submitted by Eric Martz; posted on Wednesday, December 04, 2024
I've written a new guide:
How to find the structure of a protein: https://proteopedia.org/w/How_to_find_the_structure_of_a_protein. Its suitable for students. It starts by finding the amino acid sequence in UniProt, and suggests what to consider when selecting the best model when multiple empirical models are available. And when no empirical model is available, it directs you to ...
There is also a new guide about how to be aware of Missing Residues and Incomplete Sidechains: https://proteopedia.org/w/Missing_residues_and_incomplete_sidechains. It illustrates how you can't be unaware of them in FirstGlance in Jmol, but you may well be unaware in MolStar, PyMOL, ChimeraX, or iCn3D. Then it suggests how to use AlphaFold models to fill in missing sidechain atoms or loops, so that your analysis of charge distribution is not erroneous.
Filling in missing charged atoms on the protein surface is especially important before you make an Electrostatic Potential Map, which you can do quite easily in several popular free applications: https://proteopedia.org/w/Electrostatic_potential_maps. That new page illustrates maps made in each application.
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