I want to find a proper inhibitor for an enzyme. The traditional inhibitor has been proved to construct a covalent link with the active residue of the enzyme. Is it possible to predict if my compound can construct a covalent link with the residue (using computational methods such as molecular docking)?
Actually, there are two types of molecular docking method are known. First one is non-covalent docking (flexible or rigid) and the second one is covalent docking. In this second case, small molecules can attach to the protein by a covalent bond using esterification, Michael addition reaction etc. Therefore, covalent docking may be a solution of your present problem.
Yes, there are covalent docking softwares.
the other softwares like autodock vina, autodock 4 are for non-covalent docking
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