GO terms associated to TP53 protein were chromatin binding, protein heterodimerization activity, transcription factor activity, zinc ion binding, DNA binding that were predicted by all of the tools.
(C) Ligand binding poses predicted by PharmDock for co-crystallized ligand in PDB structure 1MQ6.
Based on the binding poses predicted by molecular docking, single-point mutations were designed to test their impact on ligand binding.
The results obtained for experimental pockets (black crosses) are compared to binding sites predicted by eFindSite (blue triangles).
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.
Of the 14 conserved binding sites predicted by TargetScan, 13 were also predicted by one of the other programmes.
It is unfair to use the binding information to predict epitope sites in an unbound status.
DNA-binding residues in the TS75 dataset whose SS information was predicted by the PREDATOR program (Frishman and Argos, 1997).
