Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering.

ABSTRACT: By merging advanced dimensionality reduction (DR) and clustering algorithm (CA) techniques, our study advances the sampling procedure for predicting NMR chemical shifts (CS) in intrinsically disordered proteins (IDPs), making a significant leap forward in the field of protein analysis/modeling. We enhance NMR CS sampling by generating clustered ensembles that accurately reflect the different properties and phenomena encapsulated by the IDP trajectories. This investigation critically assessed different rapid CS predictors, both neural network (e.g., Sparta+ and ShiftX2) and database-driven (ProCS-15), and highlighted the need for more advanced quantum calculations and the subsequent need for more tractable-sized conformational ensembles. Although neural network CS predictors outperformed Pr

SUBMITTER: Bakker MJ 

PROVIDER: S-EPMC11412307 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature