There are many tools to identify the protein target for a ligand. When I start with a protein, what are the best tools to figure out the possible chemical ligand for this protein?
Hi Ahmad,
The tools involved in virtual screening based on molecular docking can meet your needs. GOLD and LeDock had the best sampling power and AutoDock Vina had the best scoring power. Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities to the entire dataset could not be well predicted by most docking programs. However, to some types of protein families, relative high linear correlations between the docking scores and experimental binding affinities could be achieved.
Hi Ahmad,
The tools involved in virtual screening based on molecular docking can meet your needs. GOLD and LeDock had the best sampling power and AutoDock Vina had the best scoring power. Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities to the entire dataset could not be well predicted by most docking programs. However, to some types of protein families, relative high linear correlations between the docking scores and experimental binding affinities could be achieved.
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