I am working on beta-lactamases and trying to find in-silico binding/affinity energy of beta-lactam antibiotics with the protein. I tried using Autodock-vina, but the order I am getting seems to be wrong. For that, I am trying to visualize if the binding is perfect or not. Any tools for that? Also, is there any free substitute for Autodock?
I presume that you are looking at a covalent adduct, as all prior experience suggests that this is necessary. This is very difficult to do in silico. The affinity is only part of the basis for efficacy and affinity is composed of initial rate reactivity as well as binding site fit. The relative importance of those components changes as a function of initial rate kinetics as well. It is essential that you have the right experimental data to build on to hope to have a useful guide to more compounds.
- Badges
- Science topic
- Similar topics
- Agricultural Science
- Agronomy
- Crop Science
- Crop