This method thus adds an element of ligand-based drug design to what is essentially a structure-based drug design method of docking and scoring.
Although docking is difficult, current methods of docking can lead to results deemed to be highly accurate in some cases.
Nevertheless, most methods of docking employ a single, rigid structure of the receptor.
This helped us to compare the effect of the partial charge calculation method on docking accuracy.
Models of toxin channel complexes were generated by the bimolecular complex generation with global evaluation, and ranking (BiGGER) docking software and selected by using a screening method of the docking solutions.
Then, the method of molecular docking is employed to screen the compound library for potential leads that can dock onto the target protein, whereas post-docking analysis serves to enrich the hit rate.
For exploring possible diuresis mechanism of E. lathyris, in this study, a potential diuresis related target, urea transporter B (UT-B), and its potential ligands were discovered by using bioinformatics method of "Inverse Docking".
At present, our studies [13] and investigations of other authors [14] using the method of molecular docking of nanosize titanium dioxide material to the extracellular domain of a number of receptors have determined potentially probable sites of binding for this nanosize material of different affinity and analyzed the character of bonds, stabilizing them according to their aminoacid composition.
Here we focus on the method of receptor-ligand docking and scoring, which can be used when a three-dimensional structure of the target is available.
As a main method of SBVS, molecular docking is the most widely used in practice, and there have reported a number of successful examples [ 2].
In this context, the methods of molecular docking, molecular dynamics (MD) simulation, and binding free energy analysis are applied to investigate and reveal the detailed binding mechanism of four roscovitine derivatives with CDK5.
