AlphaFold/Index

From Proteopedia

Here are pages in Proteopedia that relate to AlphaFold.

Introductions to AlphaFold

• AlphaFold. An introduction and overview.
• Theoretical models describes the breakthrough in structure prediction made by AlphaFold in CASP 14 (2020) and the continued pre-eminence of AlphaFold in CASP 15 [2022].

How To Make Predictions

• How to predict structures with AlphaFold when the AlphaFold Database does not already have what you want.
• Joining AlphaFold predictions for halves of a molecule, when the sequence is too long for AlphaFold to handle.
• How to renumber PDB files in order to correct sequence numbers.

Interpreting Predictions

• AlphaFold pLDDT and expected distance error
• How to get average pLDDT from AlphaFold models: When any subset of residues (such as a sequence range) is selected (using Find) in FirstGlance in Jmol, listing the found residues reports their average pLDDT.
• Calculating GDT TS the Global Distance Test Total Score, one of the metrics used for judging accuracy of predictions in the CASP competitions.
• AlphaFold3 case studies includes a case that AlphaFold3 cannot predict.

Examples of Predictions

• AlphaFold2 examples from CASP 14. A detailed 2021 analysis of several AlphaFold predictions compared with empirically-determined structures.
• AlphaFold3 case studies (November 2024) includes a case that AlphaFold3 cannot predict.

Uses of Predictions

• Missing residues and incomplete sidechains suggests using AlphaFold predicted structures, in parallel with empirical models that have missing residues or atoms, when analyzing surface characteristics such as charge distribution (electrostatic potential maps), salt bridges, cation-pi interactions, etc.
• Converting AlphaFold3 CIF to PDB

See Also

• RoseTTAFold
• wwPDB, the WorldWide Protein DataBank archive of empirical models.
• ModelArchive, a database of theoretical (non-empirical) models.