Nicholas Edmunds

Abstract Motivation: Despite an increase in the accuracy of predicted protein structures following the development of AlphaFold2, there remains a gap in the accuracy of predicted model quality assessment scores when compared to those generated with reference to experimental structures. The predictions of model accuracy scores generated by AlphaFold2, plDDT and pTM, have become familiar descriptors of model quality.

4 DISCUSSION Overall, the ModFOLDdock server variants were arguably the most successful model QA methods at CASP15, being consistently placed in the top few groups across all aspects of the EMA category of CASP15. By our own analysis, the ModFOLDdock variants were also found to highly correlate with the CASP official observed scores (e.g., oligo-lDDT) ranging from 0.73 to 0.82 as measured by the Pearson correlation coefficients.

New Results doi: https://doi.org/10.1101/2022.12.06.519289 Abstract Motivation: The accuracy gap between predicted and experimental structures has been significantly reduced following the development of AlphaFold2. However, for further studies, such as drug discovery and protein design, AlphaFold2 structures need to be representative of proteins in solution, yet AlphaFold2 was trained to generate only a few structural conformations rather than a conformational landscape.