Which statement best explains the difference between local and global docking in structure-based drug design?

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Question restatement: Which statement best explains the difference between local and global docking in structure-based drug design?

Option 1: 'Global docking is faster and more accurate than local docking because it avoids assumptions about the binding site.' This is generally false. Global docking tends to be more computationally intensive because it explores a much larger search space without prior knowledge of where the ligand binds, which can reduce efficiency and accuracy. It does not inherently avoid assumptions about the binding site; instead, it minimizes assumptions by not pre-defining the site, but that broad search often comes at the cost of speed and sometimes accuracy due to noise in the search space.

Option 2: 'Global docking always results in better ligand poses because it explores more conformational space.' This overstates the benefit. Exploring more conformational space can yield more potential poses, but it does not guarantee better or more accurate results. The quality of poses depends on scoring functions, sampling efficiency, and the complexity of the protein pocket. More space to search can also increase false positives and noise.

Option 3: 'Local docking can only be used when crystallographic structures are available for both ligand and protein.' This is incorrect. Local docking refers to dockings performed with a predefined binding site, and while accurate structures help, local docking does not strictly require crystal structures for both ligand and protein. It can be used with modeled structures or even apo proteins, provided a binding site is defined and the receptor conformation is appropriate.

Option 4: 'Local docking is used when the binding site is known, while global docking is generally necessary when the binding site is unknown.' This statement aligns with standard practice. When the site's location is known, local docking targets a specific region, making sampling more focused and often more efficient. When the site is unknown, global docking searches across the entire protein surface to identify potential binding sites, though at a higher computational cost and with different scoring challenges.

In summary, the key conceptual distinction is about prior knowledge of the binding site: if you know where the ligand should bind, local docking is appropriate; if you do not, global docking is used to discover potential binding regions. The incorrect options mischaracterize speed versus accuracy trade-offs, assumptions about necessary data, or the applicability of docking approaches in ways that conflict with common practice in structure-based drug design.

2254 BIOSC 1544 SEC1000 Quiz #24: Structure-Based CADD

Which statement best explains the difference between local and global docking in structure-based drug design?

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