Filling the gap - AlphaFill adds ligands and cofactors to AlphaFold2 predicted protein structures. NBThighlight
). To allow users to explore possibilities, we have introduced a selector in the web interface that sets the display to the desired identity level on a per-structure basis.
The global r.m.s.d. is not a good indicators of transplant quality, but is useful to get a feeling of the similarity between the donor and acceptor structures: a structure with lower global r.m.s.d. but the same or similar identity, denotes a similar conformation. This is reflected in the kinase examples .
It is good to keep in mind that the AlphaFill models are not very suitable for precise quantification of interactions between the transferred ligand and the protein . Namely, this requires coordinate precision that is not provided by either the AlphaFold or the AlphaFill models . Hence, the models should be interpreted in a qualitative manner.
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