AlphaFold/Index
From Proteopedia
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*[[How to predict structures with AlphaFold]] when the [https://alphafold.ebi.ac.uk/ AlphaFold Database] does not already have what you want. | *[[How to predict structures with AlphaFold]] when the [https://alphafold.ebi.ac.uk/ 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. | *[[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== | ==Interpreting Predictions== | ||
Revision as of 23:58, 28 September 2023
Here are pages in Proteopedia that relate to AlphaFold.
Contents |
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
- Calculating GDT TS the Global Distance Test Total Score, one of the metrics used for judging accuracy of predictions in the CASP competitions.
Examples of Predictions
- AlphaFold2 examples from CASP 14. A detailed analysis of several AlphaFold predictions compared with empirically-determined structures.
