Lauren L. Porter

The paper uses AlphaFold to identify gating residues that control conformational accessibility in proteins, finding that AlphaFold sometimes misapplies this principle.

The paper describes a protein fold switch in a bactericidal nanomachine that enables membrane puncture and bactericidal activity.

The paper evaluates AF-cluster's performance on metamorphic proteins and finds random sequence sampling outperforms it, suggesting ColabFold-based methods as a better alternative.

The paper evaluates whether AlphaFold2 can predict alternative conformations of fold-switching proteins beyond its training data using a modified model trained on a limited dataset.

This study evaluates AlphaFold2's ability to predict fold-switching proteins and finds it has limited success in sampling multiple conformations and accurately assessing confidence metrics.

The paper shows that ColabFold can predict alternative protein structures without needing coevolutionary information from clustered MSAs, using only single sequences or sequence similarity.

SSDraw generates publication-quality protein secondary structure diagrams and allows comparison of homologous proteins using color coding and alignment.

The paper identifies coevolutionary signatures in fold-switching proteins and uses them to predict alternative protein conformations using AlphaFold2.

The paper identifies an evolutionary pathway between two protein folds using statistical methods and structural models on bacterial response regulator proteins.

The paper identifies fold-switching proteins by analyzing secondary structure propensities in the NusG family, finding 25% of sequences undergo α-helix ↔ β-sheet transitions.

The paper evaluates AlphaFold2's performance on fold-switching proteins, finding it predicts one conformation accurately but misses others, despite high confidence scores.

The paper introduces a sequence-based method to predict fold-switching proteins that transition between α-helix and β-strand structures, achieving a Matthews Correlation Coefficient of 0.70.

The paper identifies evolved fold switchers from amino acid sequences by analyzing inconsistencies in secondary structure predictions between helix and strand conformations.

The paper identifies fold-switching proteins by analyzing inconsistencies in secondary structure predictions from amino acid sequences.