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, artificial intelligence (AI), and allostery

R Nussinov, M Zhang, Y Liu, H Jang - The Journal of Physical …, 2022 - ACS Publications
AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of
biological sequence data and artificial intelligence (AI). AlphaFold has appended projects …

Single-sequence protein structure prediction using a language model and deep learning

R Chowdhury, N Bouatta, S Biswas, C Floristean… - Nature …, 2022 - nature.com
AlphaFold2 and related computational systems predict protein structure using deep learning
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …

Harnessing protein folding neural networks for peptide–protein docking

T Tsaban, JK Varga, O Avraham, Z Ben-Aharon… - Nature …, 2022 - nature.com
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …

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 …

The impact of AlphaFold2 one year on

DT Jones, JM Thornton - Nature methods, 2022 - nature.com
The greatly improved prediction of protein 3D structure from sequence achieved by the
second version of AlphaFold in 2020 has already had a huge impact on biological research …

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 …

Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery

W Wilman, S Wróbel, W Bielska… - Briefings in …, 2022 - academic.oup.com
Antibodies are versatile molecular binders with an established and growing role as
therapeutics. Computational approaches to develo** and designing these molecules are …

Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader

K Zhao, Y **a, F Zhang, X Zhou, SZ Li… - Communications …, 2023 - nature.com
Recognition of remote homologous structures is a necessary module in AlphaFold2 and is
also essential for the exploration of protein folding pathways. Here, we propose a method …