Modeling conformational states of proteins with AlphaFold

D Sala, F Engelberger, HS Mchaourab… - Current Opinion in …, 2023 - Elsevier
Many proteins exert their function by switching among different structures. Knowing the
conformational ensembles affiliated with these states is critical to elucidate key mechanistic …

AlphaFold2 and its applications in the fields of biology and medicine

Z Yang, X Zeng, Y Zhao, R Chen - Signal Transduction and Targeted …, 2023 - nature.com
Abstract AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind
that can predict three-dimensional (3D) structures of proteins from amino acid sequences …

Accurate structure prediction of biomolecular interactions with AlphaFold 3

J Abramson, J Adler, J Dunger, R Evans, T Green… - Nature, 2024 - nature.com
The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of
proteins and their interactions, enabling a huge range of applications in protein modelling …

Predicting multiple conformations via sequence clustering and AlphaFold2

HK Wayment-Steele, A Ojoawo, R Otten, JM Apitz… - Nature, 2024 - nature.com
Abstract AlphaFold2 (ref.) has revolutionized structural biology by accurately predicting
single structures of proteins. However, a protein's biological function often depends on …

High-resolution de novo structure prediction from primary sequence

R Wu, F Ding, R Wang, R Shen, X Zhang, S Luo, C Su… - BioRxiv, 2022 - biorxiv.org
Recent breakthroughs have used deep learning to exploit evolutionary information in
multiple sequence alignments (MSAs) to accurately predict protein structures. However …

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning

K Stahl, A Graziadei, T Dau, O Brock… - Nature …, 2023 - nature.com
While AlphaFold2 can predict accurate protein structures from the primary sequence,
challenges remain for proteins that undergo conformational changes or for which few …

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 …

SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2

RA Stein, HS Mchaourab - PLOS Computational Biology, 2022 - journals.plos.org
The unprecedented performance of Deepmind's Alphafold2 in predicting protein structure in
CASP XIV and the creation of a database of structures for multiple proteomes and protein …

AlphaFold2 fails to predict protein fold switching

D Chakravarty, LL Porter - Protein Science, 2022 - Wiley Online Library
AlphaFold2 has revolutionized protein structure prediction by leveraging sequence
information to rapidly model protein folds with atomic‐level accuracy. Nevertheless, previous …

AFsample: improving multimer prediction with AlphaFold using massive sampling

B Wallner - Bioinformatics, 2023 - academic.oup.com
The AlphaFold2 neural network model has revolutionized structural biology with
unprecedented performance. We demonstrate that by stochastically perturbing the neural …