Protein–Ligand Docking: AlphaFold2-predicted vs. X-ray Determined Protein Structures
Structure-based drug design relies on information about the 3D structure of a protein–ligand complex for potential drug molecules and their target. This structural information is used to optimize the potency and selectivity of a drug candidate at a reduced cost. Obtaining a full picture of the protein–ligand complex first requires knowledge of the structure of the protein target. A recent breakthrough in protein structure prediction using computational methods is the AlphaFold2 (AF2) algorithm developed by DeepMind. This leads us to consider the following question:
Can AF2 predicted protein structures be used to determine the protein-ligand complex with the same degree of confidence as experimentally determined protein structures?
In this white paper, we use our validated, configurable protein–ligand docking software GOLD to compare predicted complex structures using AF2 predicted and X-ray determined protein structures. Download the free white paper to read our conclusions on the applicability of de novo predicted protein structures in SBDD.
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