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Chemistry Forums for Students => Undergraduate General Chemistry Forum => Topic started by: aBeard on March 28, 2017, 06:13:22 PM

Title: Prediction of proper ligands for the purpose of molecular docking with enzymes.
Post by: aBeard on March 28, 2017, 06:13:22 PM

Hi,
I know as much as that the enzyme should have a well defined structure to allow the enzyme to ''enter'' more easily. I also know that the interaction is stronger the more ongoing hydrogen bonding is present, and other inter molecular interaction. What I'm struggling is to predict whether a molecule will be suitable to behave as a proper ligand. Is that possible to predict without the usage of a proper software to calculate the scoring value of the complex?

Title: Re: Prediction of proper ligands for the purpose of molecular docking with enzymes.
Post by: Babcock_Hall on April 03, 2017, 04:24:59 PM

You have asked a very complicated question, and I am not sure what you mean by a "proper ligand."  One, some enzymes and some ligands change shape upon binding to each other, but not all do.  Two, many forces including electrostatic ones, are responsible for binding between a ligand an an enzyme.  Three, a few complexes are relatively easy to predict qualitatively, such as substrate analogs.  However in among substrate analogs there are some odd cases.  Perhaps a good review article on docking would be a start.

Title: Re: Prediction of proper ligands for the purpose of molecular docking with enzymes.
Post by: Babcock_Hall on April 04, 2017, 10:19:50 AM

Is this a homework problem?  There are many experimental methods available to detect binding or to localize the binding to a particular portion of a macromolecule.