A structural biology community assessment of AlphaFold2 applications

M Akdel, DEV Pires, EP Pardo, J Jänes… - Nature Structural & …, 2022 - nature.com
Most proteins fold into 3D structures that determine how they function and orchestrate the
biological processes of the cell. Recent developments in computational methods for protein …

[HTML][HTML] Progress at protein structure prediction, as seen in CASP15

A Elofsson - Current Opinion in Structural Biology, 2023 - Elsevier
In Dec 2020, the results of AlphaFold version 2 were presented at CASP14, sparking a
revolution in the field of protein structure predictions. For the first time, a purely …

[HTML][HTML] Integrative structural biology in the era of accurate structure prediction

G Masrati, M Landau, N Ben-Tal, A Lupas… - Journal of molecular …, 2021 - Elsevier
Characterizing the three-dimensional structure of macromolecules is central to
understanding their function. Traditionally, structures of proteins and their complexes have …

AlphaFold2 and the future of structural biology

P Cramer - Nature structural & molecular biology, 2021 - nature.com
To the Editor—AlphaFold2 is a machine-learning algorithm for protein structure prediction
that has now been used to obtain hundreds of thousands of protein models. The resulting …

The impact of AlphaFold Protein Structure Database on the fields of life sciences

M Varadi, S Velankar - Proteomics, 2023 - Wiley Online Library
Arguably, 2020 was the year of high‐accuracy protein structure predictions, with AlphaFold
2.0 achieving previously unseen accuracy in the Critical Assessment of Protein Structure …

AlphaFold 2: why it works and its implications for understanding the relationships of protein sequence, structure, and function

J Skolnick, M Gao, H Zhou, S Singh - Journal of chemical …, 2021 - ACS Publications
AlphaFold 2 (AF2) was the star of CASP14, the last biannual structure prediction experiment.
Using novel deep learning, AF2 predicted the structures of many difficult protein targets at or …

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

TC Terwilliger, D Liebschner, TI Croll, CJ Williams… - Nature …, 2024 - nature.com
Artificial intelligence-based protein structure prediction methods such as AlphaFold have
revolutionized structural biology. The accuracies of these predictions vary, however, and …

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 …

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 …

AlphaDesign: A de novo protein design framework based on AlphaFold

M Jendrusch, JO Korbel, SK Sadiq - Biorxiv, 2021 - biorxiv.org
De novo protein design is a longstanding fundamental goal of synthetic biology, but has
been hindered by the difficulty in reliable prediction of accurate high-resolution protein …