[HTML][HTML] AlphaFold and implications for intrinsically disordered proteins
Accurate predictions of the three-dimensional structures of proteins from their amino acid
sequences have come of age. AlphaFold, a deep learning-based approach to protein …
sequences have come of age. AlphaFold, a deep learning-based approach to protein …
Protein design: From the aspect of water solubility and stability
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …
sequence and 3D-conformation. Their manipulation represents important aspects of the …
Large language models generate functional protein sequences across diverse families
Deep-learning language models have shown promise in various biotechnological
applications, including protein design and engineering. Here we describe ProGen, a …
applications, including protein design and engineering. Here we describe ProGen, a …
Evolutionary-scale prediction of atomic-level protein structure with a language model
Recent advances in machine learning have leveraged evolutionary information in multiple
sequence alignments to predict protein structure. We demonstrate direct inference of full …
sequence alignments to predict protein structure. We demonstrate direct inference of full …
[PDF][PDF] Language models of protein sequences at the scale of evolution enable accurate structure prediction
Large language models have recently been shown to develop emergent capabilities with
scale, going beyond simple pattern matching to perform higher level reasoning and …
scale, going beyond simple pattern matching to perform higher level reasoning and …
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 …
Computed structures of core eukaryotic protein complexes
INTRODUCTION Protein-protein interactions play critical roles in biology, but the structures
of many eukaryotic protein complexes are unknown, and there are likely many interactions …
of many eukaryotic protein complexes are unknown, and there are likely many interactions …
Language models enable zero-shot prediction of the effects of mutations on protein function
Modeling the effect of sequence variation on function is a fundamental problem for
understanding and designing proteins. Since evolution encodes information about function …
understanding and designing proteins. Since evolution encodes information about function …