Molecular models obtained from structure-based docking rationalized the enzymatic data.
The second takeaway from these two studies is that for any structure-based docking model to be successful, multiple co-binding peptides will need to be considered when docking any drug of interest.
In this study, we are employing structure-based docking [38] to predict and analyze the molecular interactions between different drugs and the relatively common HLA-B*57 01 HLA-B*57 01
In the second case, a ligand-based screen would return molecules that resemble the structure-based docking hits.
We first used LBDS (Ligand-Based Docking System) and SBDS (Structure-Based Docking System) to develop the small-molecule Smac-mimetic IAP antagonist, which was designed to bind to the BIR3 domain of IAP family members, as well as EGFR.
We combined a ligand-based pharmacophore design with a structure-based protein/ligand docking using the software MOE in order to evaluate the underlying structure/activity relationship.
Structure-based molecular docking using Glide and the human VDR structure (PDB code 1S19): (a) Docking results for all compounds with their associated XP docking and eModel scores, mechanism and experimental AC50 values; (b) Binding modes of calcipotriol (red) and proflavine hydrochloride (blue) superimposed in the binding site.
Moreover, we applied structure-based 3D docking and molecular dynamics simulations to predict and analyze the binding modes of our experimental hits (including both agonists and antagonists).
The authors used a combination of ligand-based screening and structure-based molecular docking to identify several compounds, with acyclovir predicted as most active, for experimental assays [42].
Their prediction system uses four ligand-based methods (SVM classification, SVR affinity prediction, nearest neighbors interpolation, and shape similarity) and two structure-based methods (docking and pharmacophore match).
The structure-based molecular docking is considered a suitable approach for the development of new drugs, since this approach is targeted to specific protein and specific pathway [47].
