Assessment of AlphaFold2 for Human Proteins via Residue Solvent Exposure

As only 35% of human proteins feature (often partial) PDB structures, the protein structure prediction tool AlphaFold2 (AF2) could have massive impact on human biology and medicine fields, making independent benchmarks of interest. We studied AF2’s ability to describe the backbone solvent exposure a...

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Bibliographic Details
Published in:Journal of chemical information and modeling 2022-07, Vol.62 (14), p.3391-3400
Main Authors: Bæk, Kristoffer T., Kepp, Kasper P.
Format: Article
Language:English
Subjects:
Amino acids
Computational Biochemistry
Exposure
Ligands
Monomers
Proteins
Residues
Solvents
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Summary:As only 35% of human proteins feature (often partial) PDB structures, the protein structure prediction tool AlphaFold2 (AF2) could have massive impact on human biology and medicine fields, making independent benchmarks of interest. We studied AF2’s ability to describe the backbone solvent exposure as a functionally important and easily interpretable “natural coordinate” of protein conformation, using human proteins as test case. After screening for appropriate comparative sets, we matched 1818 human proteins predicted by AF2 against 7585 unique experimental PDBs, and after curation for sequence overlap, we assessed 1264 comparative pairs comprising 115 unique AF2 structures and 652 unique experimental structures. AF2 performed markedly worse for multimers, whereas ligands, cofactors, and experimental resolution were interestingly not very important for performance. AF2 performed excellently for monomer proteins. Challenges relating to specific groups of residues and multimers were analyzed. We identified larger deviations for lower-confidence scores (pLDDT), and exposed residues and polar residues (e.g., Asp, Glu, Asn) being less accurately described than hydrophobic residues. Proline conformations were the hardest to predict, probably due to a common location in dynamic solvent-accessible parts. In summary, using solvent exposure as a metric, we quantified the performance of AF2 for human proteins and provided estimates of the expected agreement as a function of ligand presence, multimer/monomer status, local residue solvent exposure, pLDDT, and amino acid type. Overall performance was found to be excellent.
ISSN:1549-9596
1549-960X
DOI:10.1021/acs.jcim.2c00243