They found that all the tested scoring functions could not provide reliable predictions because they all failed to correlate the experimental binding affinities (pK d ) with the scores predicted by the corresponding scoring function, with the highest correlation of only − 0.32.
Out of those 41 (=4+37), 28 SNPs had the matching TF bound (PWM score P < 0.001 BH corrected) to one of the alleles, and in each of these cases a significant (P < 0.05, BH corrected) change in binding score was predicted by is-rSNP.
Although the rank order of cellulase-lignin binding predicted by hydrophobic patch score is not directly reflected in our experiments, all three cellulases contain significant hydrophobic patches predicted to impact enzyme-lignin binding [ 25].
(C) Ligand binding poses predicted by PharmDock for co-crystallized ligand in PDB structure 1MQ6.
Evaluation of the results was performed by sorting the binding energy predicted by docking conformations.
The chemical shift changes upon H3K4me3 binding also supported the binding site predicted by structural comparison.
Precision was measured as the fraction of correctly predicted TP binding sites (experimentally verified) among all binding sites predicted by the classifier to be TP binding site.
Third, within the 300-nucleotide sequence upstream of the protein-coding region, individual TF binding sites were predicted by the maximum PWM score above the threshold because about 95% of TF binding sites were known to exist in these regions.
Table 2 (full breakdown in ESI Table 4 †) reports the results of the free energy calculations based on the lowest energy docked poses, along with the RMSD of the poses with respect to the crystal ones and the binding free energy predicted by the docking scoring function for the same ligand.
These results were in close agreement with the fitness score predicted using X-score, a consensus based scoring function to calculate the binding affinity.
