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Based on our PASTA predictions and docking searches (see above), however, the self-adhesive region was identified as the overlapping Tyr-7 to Arg-12 sequence, which likely forms an antiparallel β-sheet in aqueous environments.

Therefore, in the case of homodimers (1A2K, 1AKJ, 1EER, 1IB1, 1ML0) predictions and docking were performed on the dimer rather than the monomer, to prevent the dimer interface from being predicted.

Used together with expert knowledge in the interpretation of interface predictions and docking results, prediction-driven docking is a powerful new tool in the generation of new hypotheses on the atomic details of macromolecular interactions.

Model quality was assessed relative to the crystal structure in terms of structural accuracy as well as performance in two typical structure-based drug design applications: ligand binding pose prediction and docking enrichment in virtual screening.

Our results indicate that while homology models that are reasonably accurate structurally can be constructed, without significant refinement homology models will be outperformed by crystal structures in ligand binding pose prediction and docking enrichment regardless of the template used, primarily due to the extremely high level of structural accuracy needed for such applications.

A retrosynthetic approach was employed using MOE/RECAP, followed by target prediction and docking of the resulting library against the desired targets.

Substructure analysis was performed on compounds having a favorable assessment by target prediction and docking (i.e. those compounds whose docking scores were below the threshold for all three targets).

Fig. 1 The computational strategy for rational design of A1R/A2AR PDE10A multi-target ligands started with a focused chemical space consisting of known actives of A1R, A2AR and PDE10A, and formed new synthetically feasible compounds which were subjected to target prediction and docking for synthesis and pharmacological evaluation.

Hence, in this work we describe a computational method for the design of synthetically feasible ligands that bind to A1 and A2A receptors and inhibit phosphodiesterase 10A (PDE10A), involving a retrosynthetic approach employing in silico target prediction and docking, which may be generally applicable to multi-target compound design at several target classes.

Protein-ligand binding site prediction and docking studies were performed with AnFAEA (PDB Code: 1uwc).

This study combines two of these computational approaches, interface prediction and docking.