I want to dock a number of ligands against proteins involved in the NOTCH signalling pathway. I have checked the UniProtKB and PDB database to retrieve the NOTCH1-4 _Musmusculus protein structures. The structures of short fragments of the NOTCH1-Musmusculus are available in PDB but not for the whole protein. Yet, alpha fold-predicted structures of the complete proteins NOTCH1-4 are available on UniProtKB.
Now, I need to know, if it is fine to use the alpha-fold predicted structure for docking or do I have to generate protein models. If I have to develop the models which programs shall I use considering that the complete 3D structure of the protein is not determined but of the small fragments?
Check the quality of AlphaFold models at Uniprot, especially the active site or the region of interest (by structural superimposition with solved structures that have good resolution
I will recommend you predict the whole tertiary structure rather than using the available alpha fold model.
You can use servers like RaptorX, iTASSER and others for the prediction. You can then proceed to the prediction of the active site residues using tools like CASTP and DogSite if it is unavailable in literature.
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