The binding residues for hPD-L1 on hPD-1 are colored in cyan, whereas residues contacted by the pembrolizumab VH or VL are colored in limon or orange, respectively, and the residues that contacts with both VH and VL are colored in hotpink.
The binding residues for hPD-1 on hPD-L1 are colored in red, whereas residues contacted by the avelumab VH or VL are colored in yellow or blue, respectively, and the overlapping residues used by both the receptor hPD-1 and avelumab are colored in green.
These data indicated that our method could predict binding residues for these two ligands.
We believe that metaDBSite will become a useful tool for predicting protein-DNA binding residues for relevant researchers.
Ligand binding residues for each protein were retrieved from PDBe (http://www.ebi.ac.uk/pdbe/) or were predicted using 3DLigandSite [ 41].
The binding residues for stem IA are inferred from alanine mutants (in red) (Daugherty et al., 2008 ).
Most of binding residues for the top three compounds were below 0.5, suggesting that the structure of ApoE4 will not affect ligands binding to the active site.
Ligand binding residues, for each of the ligand-bound forms of each of the structural entries of OBPs mentioned above, were identified using LIGPLOT.
In Paramecium, the binding residues for phalloidin [ 39, 40] are only well conserved in several members of the actin1subfamily (Table 4, Fig. 3).
Interestingly, CD154 can interact with both CD40 and α5β1 concomitantly, as co-incubation of sCD154 with soluble CD40 does not affect binding to α5β1, indicating that CD40 and α5β1 share distinct binding residues for CD154 [ 20, 21].
