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 …

Mechanisms and pathology of protein misfolding and aggregation

N Louros, J Schymkowitz, F Rousseau - Nature Reviews Molecular Cell …, 2023 - nature.com
Despite advances in machine learning-based protein structure prediction, we are still far
from fully understanding how proteins fold into their native conformation. The conventional …

Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

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 …

AlphaFold2 can predict single-mutation effects

JM McBride, K Polev, A Abdirasulov, V Reinharz… - Physical Review Letters, 2023 - APS
AlphaFold2 (AF) is a promising tool, but is it accurate enough to predict single mutation
effects? Here, we report that the localized structural deformation between protein pairs …

Structural analysis and architectural principles of the bacterial amyloid curli

M Sleutel, B Pradhan, AN Volkov, H Remaut - Nature Communications, 2023 - nature.com
Two decades have passed since the initial proposition that amyloids are not only (toxic)
byproducts of an unintended aggregation cascade, but that they can also be produced by an …

Structure‐Based Drug Discovery with Deep Learning

R Özçelik, D van Tilborg, J Jiménez‐Luna… - …, 2023 - Wiley Online Library
Artificial intelligence (AI) in the form of deep learning has promise for drug discovery and
chemical biology, for example, to predict protein structure and molecular bioactivity, plan …

Generative modeling, design, and analysis of spider silk protein sequences for enhanced mechanical properties

W Lu, DL Kaplan, MJ Buehler - Advanced Functional Materials, 2024 - Wiley Online Library
Spider silks are remarkable materials characterized by superb mechanical properties such
as strength, extensibility, and lightweightedness. Yet, to date, limited models are available to …

Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates

AV Fonin, IA Antifeeva, IM Kuznetsova… - Essays in …, 2022 - portlandpress.com
The facts that many proteins with crucial biological functions do not have unique structures
and that many biological processes are compartmentalized into the liquid-like biomolecular …

Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations

BP Brown, RA Stein, J Meiler… - Journal of Chemical …, 2024 - ACS Publications
Protein thermodynamics is intimately tied to biological function and can enable processes
such as signal transduction, enzyme catalysis, and molecular recognition. The relative free …