Dear friends,
We generaly use density functional theory to find the interactions between two small molecules (in homo dimer and hetero dimer). During the dimerization, we choose the hydrogen bonding sites based on the electrophilic and nucleophilic sites. I just tried to do the same with Autodock which is useful for protein-ligand interactions and where the genetic algorithm is employed. When I perform the docking of two small molecules, I deleted the protein (instead of ligand), metal and solvents in the protein file and dock with another ligand. Finally I get 10 conformations of ligand-ligand complex. Could you please someone comment how reliable the genetic algorithm for finding the interactions between two small molecules?
can we use the highest negative binding energy complex for further DFT calculations?
Although I never used the ligand-ligand interaction, on basis of general rule in the docking process, it should be reliable your calculations. I think, no matter if there is protein-ligand or ligand-ligand interactions.
Usually for smaller sized entity (MW 1K) the results are reliable, more than enough for the purpose! However, you have to be cautious with the number of components in the simulation process!
Some references you might like to consider:
https://www.sciencedirect.com/science/article/pii/S0959440X96800790
https://www.ncbi.nlm.nih.gov/pubmed/8728656
Article Genetic Algorithms for Protein Structure Prediction
Try the method of Gumbart, Roux, and Chipot for protein-protein or protein-ligand interactions. But it's not genetic.
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