What is the primary purpose of molecular docking in structure-based drug discovery?

Question

BlackTom AI · Accepted Answer

In approaching this question, consider what molecular docking is designed to accomplish within structure-based drug discovery.
Option A posits that the main goal is to cluster ligand poses by RMSD and generate pharmacophores from those clusters. While pose clustering can be used in some workflows to analyze docking results or aid pharmacophore modeling, it is not the primary purpose of docking itself. Docking centers on predicting how a ligand fits into a binding site and scoring those poses, not on clustering results for pharmacophore generation.
Option B suggests that docking aims to simulate the full thermodynamic profile of ligand binding using molecular dynamics trajectories. This describes a detailed MD or free-energy calculation approach, which is more computationally intensive and conceptually distinct from standard docking. Docking typically uses static or semi-flexible representations and scoring functions, not a full thermodynamic MD-based profile.
Option C states: 'To predict a binding pose and generate a score that hopefully correlates with binding affinity.' This captures the core purpose of molecular docking: proposing a plausible pose of the ligand in the binding site and providing a qualitative or quantitative score that is used as a proxy for binding affinity, guiding prioritization of compounds. The language acknowledges that the correlation with actual affinity is imperfect, which aligns with how docking is used in practice.
Putting the pieces together, Option C accurately reflects the principal objective of molecular docking, while Options A and B describe related techniques or outcomes that are not the primary aim of docking as commonly defined in structure-based drug discovery.

2254 BIOSC 1544 SEC1000 Quiz #22: CADD and Protein Flexibility

What is the primary purpose of molecular docking in structure-based drug discovery?

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