The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins
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 …
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 …
relevant data can accurately predict structures.•Algorithmic advances can harness …
AlphaFold predictions of fold-switched conformations are driven by structure memorization
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 …
accurately infer protein structure from sequence–may discern important features of folded …
Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
Recent advances and challenges in protein structure prediction
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 …
in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated …
How can we discover developable antibody-based biotherapeutics?
Antibody-based biotherapeutics have emerged as a successful class of pharmaceuticals
despite significant challenges and risks to their discovery and development. This review …
despite significant challenges and risks to their discovery and development. This review …
Distinguishing features of fold‐switching proteins
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 …
small‐but‐increasing number remodel their secondary and tertiary structures and change …
[HTML][HTML] AlphaFold2 has more to learn about protein energy landscapes
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 …
accurately infer protein structure from sequence–may discern important features of folded …
Structural modeling of antibody variable regions using deep learning—progress and perspectives on drug discovery
I Jaszczyszyn, W Bielska, T Gawlowski… - Frontiers in Molecular …, 2023 - frontiersin.org
AlphaFold2 has hallmarked a generational improvement in protein structure prediction. In
particular, advances in antibody structure prediction have provided a highly translatable …
particular, advances in antibody structure prediction have provided a highly translatable …
The effects of codon usage on protein structure and folding
MKJ Moss, LM Chamness… - Annual Review of …, 2023 - 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 …
the synonymous codons encoding the protein sequence. Synonymous codon substitutions …