First, there is a striking overlap between p63 and p73 targets (Tables S1 and S2), and a strong correlation between p63 and 73 binding scores based on the genome-wide array data (Fig. 2).
4) The HLA annotation score, based on the predicted IC50 binding affinities from NetMHC server, is used to associate peptides with particular HLA alleles.
Then, every ligand and binding site residue is given a score and classified by that score based on the following algorithm (see also Figure 1): For each residue and component of each ligand and each binding site, the initial score is defined to be 0.
We used MM/PBSA [ 35, 36] to calculate the absolute binding free energy and compared it with the Glide [ 32] score based on the 10 ns MD simulation.
It also calculates an off-target hit score based on the number, position, and distribution of mismatches to predicted off-target sequences (scores reflect probability of gRNA binding).
First, IGF-binding proteins received high topological scores based on both microarray and iTRAQ data.
They used four docking programs (FlexX, GOLD, Glide, and Molegro) to investigate the performance of docking and the correlation of docking scores based on the binding affinity data between wild-type and mutant-type forms.
Two heterogeneous data sources, miRNA-target prediction scores based on target binding and the sample-matched expression profiles of miRNA and mRNA, are integrated to extract the coherent miRNA mRNA modules.
The surfaces were scored based on biocompatibility and probe binding capacity as judged by spot morphology, signal intensities, signal to noise ratios, dynamic range, sensitivity, and reproducibility.
