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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 …
Accurate structure prediction of biomolecular interactions with AlphaFold 3
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 …
proteins and their interactions, enabling a huge range of applications in protein modelling …
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 …
High-resolution de novo structure prediction from primary sequence
Recent breakthroughs have used deep learning to exploit evolutionary information in
multiple sequence alignments (MSAs) to accurately predict protein structures. However …
multiple sequence alignments (MSAs) to accurately predict protein structures. However …
Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning
While AlphaFold2 can predict accurate protein structures from the primary sequence,
challenges remain for proteins that undergo conformational changes or for which few …
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
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 …
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 …
CASP XIV and the creation of a database of structures for multiple proteomes and protein …
AlphaFold2 fails to predict protein fold switching
AlphaFold2 has revolutionized protein structure prediction by leveraging sequence
information to rapidly model protein folds with atomic‐level accuracy. Nevertheless, previous …
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 …
unprecedented performance. We demonstrate that by stochastically perturbing the neural …