Modeling conformational states of proteins with AlphaFold
Many proteins exert their function by switching among different structures. Knowing the
conformational ensembles affiliated with these states is critical to elucidate key mechanistic …
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 …
that can predict three-dimensional (3D) structures of proteins from amino acid sequences …
Predicting multiple conformations via sequence clustering and AlphaFold2
Abstract AlphaFold2 (ref.) has revolutionized structural biology by accurately predicting
single structures of proteins. However, a protein's biological function often depends on …
single structures of proteins. However, a protein's biological function often depends on …
Sampling alternative conformational states of transporters and receptors with AlphaFold2
Equilibrium fluctuations and triggered conformational changes often underlie the functional
cycles of membrane proteins. For example, transporters mediate the passage of molecules …
cycles of membrane proteins. For example, transporters mediate the passage of molecules …
Mega-scale experimental analysis of protein folding stability in biology and design
Advances in DNA sequencing and machine learning are providing insights into protein
sequences and structures on an enormous scale. However, the energetics driving folding …
sequences and structures on an enormous scale. However, the energetics driving folding …
A structural biology community assessment of AlphaFold2 applications
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 …
biological processes of the cell. Recent developments in computational methods for protein …
Before and after AlphaFold2: An overview of protein structure prediction
LMF Bertoline, AN Lima, JE Krieger… - Frontiers in …, 2023 - frontiersin.org
Three-dimensional protein structure is directly correlated with its function and its
determination is critical to understanding biological processes and addressing human …
determination is critical to understanding biological processes and addressing human …
Harnessing protein folding neural networks for peptide–protein docking
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …
Machine learning-guided protein engineering
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …
machine learning methods. These methods leverage existing experimental and simulation …
AlphaFold2 models indicate that protein sequence determines both structure and dynamics
Abstract AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can
visualize, analyze and interpret the structures and functions of all proteins solely from their …
visualize, analyze and interpret the structures and functions of all proteins solely from their …