Ethan A. Chen

Sequence clustering confounds AlphaFold2

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.

AlphaFold2 has more to learn about protein energy landscapes

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.

Colabfold predicts alternative protein structures from single sequences, coevolution unnecessary for AF-cluster

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: software for generating comparative protein secondary structure diagrams

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