The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins

V Agarwal, AC McShan - Nature Chemical Biology, 2024 - nature.com
Artificial intelligence-driven advances in protein structure prediction in recent years have
raised the question: has the protein structure-prediction problem been solved? Here, with a …

AlphaFold, allosteric, and orthosteric drug discovery: Ways forward

R Nussinov, M Zhang, Y Liu, H Jang - Drug discovery today, 2023 - Elsevier
Highlights•AlphaFold models have rigid protein structures.•Advanced deep algorithms fed
relevant data can accurately predict structures.•Algorithmic advances can harness …

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 …

Pragmatic coarse-graining of proteins: models and applications

L Borges-Araújo, I Patmanidis, AP Singh… - Journal of Chemical …, 2023 - ACS Publications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

Recent advances and challenges in protein structure prediction

CX Peng, F Liang, YH **a, 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 …

[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 …

The effects of codon usage on protein structure and folding

MKJ Moss, LM Chamness… - Annual Review of …, 2024 - annualreviews.org
The rate of protein synthesis is slower than many folding reactions and varies depending on
the synonymous codons encoding the protein sequence. Synonymous codon substitutions …

[HTML][HTML] Context-dependent, fuzzy protein interactions: Towards sequence-based insights

M Fuxreiter - Current Opinion in Structural Biology, 2024 - Elsevier
Predicting protein interactions in the cellular environment still remains a challenge in the
AlphaFold era. Protein interactions, similarly to their structures, sample a continuum from …

How can we discover developable antibody-based biotherapeutics?

J Bauer, N Rajagopal, P Gupta, P Gupta… - Frontiers in Molecular …, 2023 - frontiersin.org
Antibody-based biotherapeutics have emerged as a successful class of pharmaceuticals
despite significant challenges and risks to their discovery and development. This review …

Medicinal chemistry strategies for the modification of bioactive natural products

Y Ding, X Xue - Molecules, 2024 - mdpi.com
Natural bioactive compounds are valuable resources for drug discovery due to their diverse
and unique structures. However, these compounds often lack optimal drug-like properties …