![]() In order to accomplish this task, molecular docking tools will generate a set of different ligand binding poses and use a scoring function to estimate binding affinities for the generated ligand poses in order to determine the best binding mode. Where the term "binding pose" considers the orientation of a ligand relative to its receptor as well as the ligand's conformation. Typically, the goals of molecular docking are the identification of a ligand that binds to a specific receptor binding site and the identification of its preferred, energetically most favorable, binding pose. I would be happy to hear your comments and suggestions. Here, I want to briefly summarize the idea of molecular docking, and give a short overview about how we can use AutoDock 4.2's hybrid approach for evaluating binding affinities. Discussions and questions about methods, approaches, and tools for estimating (relative) binding free energies of protein-ligand complexes are quite popular, and even the simplest tools can be quite tricky to use.
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