To obtain a predicted affinity for a given peptide, the three peptide:MHC models were evaluated in the pair-potential, and the final binding score was obtained as the simple average of the three binding scores.
Only the binding pose with the highest binding score was selected for further consideration.
All the compounds (1 3) were found similar according to their binding pattern to IL-2 protein in molecular docking studies but the binding score was lowest for metabolite 2. 13065_2013_700_MOESM1_ESM.doc Additional file 1 Table S1: 1H NMR (300 MHz, CDCl3)a) chemical shifts of compound 1 and its metabolites 2 and 3. δ in ppm and J in Hz.
On the other hand, compound 10 which does not affect platelet aggregation (Figure 4B), did not interact with Tyr 355 (Figure 8C) although its binding score was −7.2 kcal/mol (−6.8 kcal/mol for the (S) enatiomer).
The only SH3 domain-containing protein that in addition to CIN85 and CD2AP showed a significant yet four-fold weaker binding score was Grb2.
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.
The molecule shown in red is the docked pose with the multi-objective strategy, and the binding score is −12.54 (force-filed-based score), −9.75 (empirical-based score) and −138.84 (knowledge-based score), and the latter two are close to the score values of the native pose.
The monomers giving the highest binding score were further tested using simulated annealing in order to mimic the complexation of the functional monomers with template in the monomer mixture.
The Ki-67, p27, and PCNA to the CDK1 binding score are 20.92, 21.72, and 24.32, respectively by the ZDOCK program.
The conformations with the overall highest binding score were chosen for display here.
