ArticlebioRxiv : the preprint server for biology2025
Using AlphaFold2 to Predict the Conformations of Side Chains in Folded Proteins.
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
AlphaFold has revolutionized protein structure prediction by accurately creating 3D structures from just the amino acid sequence. However, even with extensive research validating its overall accuracy, a key question remains: Can AlphaFold predict the conformation of individual amino acid residue side chains within a folded protein? This is important for the field of molecular modeling, particularly when predicting the effects of mutations on protein stability and ligand binding. AlphaFold generates a set of atomic coordinates not just for the mutated side chain but also for potential rearrangements across the entire protein structure. In this study we investigate the ability of ColabFold, an online implementation of AlphaFold2 (AF2), to predict the conformations of residue side chains in folded proteins. We find that over a set of 10 benchmark proteins, the side chain conformation prediction error of ColabFold is on average
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