Recent advances and challenges in protein structure prediction

CX Peng, F Liang, YH Xia, KL Zhao… - Journal of Chemical …, 2023 - ACS Publications
Artificial intelligence has made significant advances in the field of protein structure prediction
in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated …

Distinguishing features of fold‐switching proteins

D Chakravarty, JW Schafer, LL Porter - Protein Science, 2023 - Wiley Online Library
Though many folded proteins assume one stable structure that performs one function, a
small‐but‐increasing number remodel their secondary and tertiary structures and change …

AlphaFold predictions of fold-switched conformations are driven by structure memorization

D Chakravarty, JW Schafer, EA Chen, JF Thole… - Nature …, 2024 - nature.com
Recent work suggests that AlphaFold (AF)–a deep learning-based model that can
accurately infer protein structure from sequence–may discern important features of folded …

SSDraw: software for generating comparative protein secondary structure diagrams

EA Chen, LL Porter - Protein Science, 2023 - Wiley Online Library
The program SSDraw generates publication‐quality protein secondary structure diagrams
from three‐dimensional protein structures. To depict relationships between secondary …

[HTML][HTML] AlphaFold2 has more to learn about protein energy landscapes

D Chakravarty, JW Schafer, EA Chen, JR Thole… - BioRxiv, 2023 - ncbi.nlm.nih.gov
Recent work suggests that AlphaFold2 (AF2)–a deep learning-based model that can
accurately infer protein structure from sequence–may discern important features of folded …

[HTML][HTML] Metamorphic proteins and how to find them

LL Porter, I Artsimovitch… - Current opinion in …, 2024 - Elsevier
In the last two decades, our existing notion that most foldable proteins have a unique native
state has been challenged by the discovery of metamorphic proteins, which reversibly …

[HTML][HTML] ColabFold predicts alternative protein structures from single sequences, coevolution unnecessary for AF-cluster

LL Porter, D Chakravarty, JW Schafer, EA Chen - bioRxiv, 2023 - ncbi.nlm.nih.gov
Though typically associated with a single folded state, globular proteins are dynamic and
often assume alternative or transient structures important for their functions 1, 2. Wayment …

Fluid protein fold space and its implications

LL Porter - Bioessays, 2023 - Wiley Online Library
Fold‐switching proteins, which remodel their secondary and tertiary structures in response
to cellular stimuli, suggest a new view of protein fold space. For decades, experimental …

A contact‐based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold‐switch

J González‐Higueras, MI Freiberger… - Protein …, 2024 - Wiley Online Library
Fold‐switching enables metamorphic proteins to reversibly interconvert between two highly
dissimilar native states to regulate their protein functions. While about 100 proteins have …

Metamorphic protein folding as evolutionary adaptation

AF Dishman, BF Volkman - Trends in Biochemical Sciences, 2023 - cell.com
Metamorphic proteins switch reversibly between multiple distinct, stable structures, often
with different functions. It was previously hypothesized that metamorphic proteins arose as …