I am using Molegro Virtual Docker for molecular docking wherein the user can render flexibility of the chains of the receptor by softening the potential. This is usually done by increasing the side-chain flexibility tolerance. I would like to know what advantage does this feature provide and how does it affect the authenticity of the result?
"In MVD, sidechain flexibility is implemented by softening the potential during the docking (by increasing the tolerance of the PLP-potentials or by weakening selected sidechains interactions), docking a diverse set of poses, and finally optimizing the sidechain configurations. It is also possible to manually minimize a receptor structure."
You may read this to know more about: http://molexus.io/mvd-features/
"A “soft” scoring function was created by attenuating the repulsive term in the Lennard-Jones potential, allowing for a closer approach between ligand and protein."
Source: Article Soft Docking and Multiple Receptor Conformations in Virtual Screening
No binding site is perfectly rigid, every binding site has a certain degree of plasticity, and this can be modeled with softened potentials, which allow obtaining docking poses for ligands that prefer slightly different conformational states of the binding site. The resulting protein-ligand complexes should be geometrically optimized, which should resolve all apparent intermolecular clashes without distorting the structure, before (re)scoring.
Docking, whatever the algorithm and platform, only makes sense for proteins with known structures (x-rays, NMR, etc.) with their bound water molecules. If you use modeled proteins, you must first subject them to a few cycles of molecular dynamics in water. If so, you can accept the results considering what Martin said.
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