Sentence examples for structure-based docking from inspiring English sources
The structure-based docking may be capturing structural information encoded in the co-crystal structure; however, as the conformation was crystallized in the presence of a G protein mimetic nanobody, what if any biased structural information was exploited by virtual screening remains opaque.
Molecular models obtained from structure-based docking rationalized the enzymatic data.
Furthermore, the carboxylic acid group of AA binding to R67 and R70 of mPGES-1 was identified by X-ray structure-based docking and mutagenesis.
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.
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).
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.
IPS-02001 (6,7-Dichloro-2,3,5,8-tetrahydroxy-1,4-naphthoquinone) was screened from different compound libraries (InterBioScreen, Commercial libraries) using an in silico structure-based molecular docking simulation method and a protein chip-based protein-protein interaction assay system.
In present study, based on the thiamin diphosphate (ThDP) site, four novel hit compounds with high inhibitory activity against the PDHc-E1 from Escherichia coli were firstly designed by using structure-based molecular docking methods.
