What is the main advantage of the relaxed complex scheme in structure-based drug discovery?

Question

BlackTom AI · Accepted Answer

To tackle this question, I’ll evaluate what each option suggests about the relaxed complex scheme in structure-based drug discovery and compare them to the core idea behind this approach.
Option 1: It accounts for protein flexibility by docking each compound into a set of diverse receptor conformations. This aligns with the relaxed complex scheme, which acknowledges that proteins are dynamic and uses multiple receptor conformations to better capture potential binding modes and improve docking accuracy. By docking across a diverse ensemble, it embodies the concept of receptor flexibility being integral to ligand binding.
Option 2: It uses probe-based druggability predictions to pre-rank ligand libraries before docking. While probe-based or druggability assessments exist in drug discovery, the relaxed complex scheme specifically centers on handling protein flexibility during docking, not on pre-ranking libraries with probe-based predictions as its defining feature. This makes the statement less representative of the relaxed complex approach.
Option 3: It reduces the conformational ensemble to a single centroid structure before scoring docked poses. This option directly contradicts the fundamental premise of the relaxed complex scheme. The scheme purposefully preserves multiple receptor conformations to capture dynamic binding scenarios, rather than collapsing them to one static structure.
Option 4: It filters docking results based on RMSF-derived flexibility scores of binding site residues. Although analyzing residue flexibility (e.g., RMSF) can inform understanding of dynamics, using RMSF-derived scores as a filtering mechanism is not the defining characteristic of the relaxed complex scheme. The core idea is ensemble docking across multiple conformations, not a post-docking filter based on fluctuation metrics.
Option 5: It applies PCA to identify dominant binding poses across protein-ligand complexes. Principal component analysis can be used to analyze binding pose diversity, but using PCA to identify dominant poses is not the central feature of the relaxed complex scheme. The scheme emphasizes docking into multiple receptor states than performing a dimensionality reduction of poses to identify dominant ones.
In summary, among the choices, option 1 most directly captures the principal advantage of the relaxed complex scheme by explicitly incorporating receptor flexibility through docking into a diverse set of receptor conformations, while the other options describe methods or goals that are not defining traits of this approach.

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

What is the main advantage of the relaxed complex scheme in structure-based drug discovery?

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