The molecular docking of ruthenium complexes 1, 2, and 3 with the active site pocket residues of human DNA TOP1 was performed using LibDock.
Based on molecular docking analysis of complexes between flavone and the c-myc G-quadruplex, we designed and screened 30 flavone derivatives containing various side chains that could potentially form interactions with the G-quadruplex grooves.
Molecular docking of La III) complex relating to HSA was investigated and confirmed the experimental results.
Molecular docking study indicated that complexes 14 and 17 could bind to the colchicine site of tubulin.
The results obtained may be a good proof of concept for implementation of molecular docking to calculate model complexes of proteins with (bio polymers of 6.4 105.5 kg/mol.
Further, the molecular docking studies confirmed that complex 1 bind to the minor groove of DNA having AT-rich sequences with relative binding energy of −196.72 kJ mol−1.
Since both uncompetitive and mixed inhibition result in the formation of an Enzyme-Substrate-inhibitor complex, molecular docking studies (using AutoDock Vina) were performed, to identify potential allosteric binding site for these compounds.
To predict the binding mode of the complex, molecular docking simulations were performed with AutoDock 4.0[32], [33] docking tool.
Molecular docking of the RecA dsDNA complex (PDB entry 3CMX) in the EM reconstruction of the RecA RecX dsDNA filament confirms that RecX can interact with both protein and nucleic acid components of the filament through its concave surface.
