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To evaluate the binding affinity and sites of nicotine and nicotyrine with the MMS19 protein, we used Autodock Vina 1.2.2 (http://autodock.scripps.edu/). The 3D crystal structure of MMS19 was obtained from the AlphaFold protein structure database (https://alphafold.ebi.ac.uk/entry/Q96...
45,46 Auto Dock Tools utilities65 were used to prepare the input files for Auto Dock 4. The Lamarckian genetic algorithm was used for a 20-run search for each compound using 1.75 million energy evaluation. For ICM, a thoroughness of 2 was used for the search algorithm. The ChemPLP ...
Next, we used four different approaches (AutoDock4.2, CRDOCK, AutoDock Vina and Dock6.3) to dock GMDP onto the R2 structure using a grid box centered on the Nη2 atom of Arg271 side chain (see details in Methods and Supplementary information). The ligand showed very similar poses in ...
Computational techniques have provided the field of drug discovery with enormous advances over the last decades. The development of methods covering dynamical aspects in protein–ligand binding is currently leading computer-aided drug design to new levels of complexity as well as accuracy. In this book...