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 …
OpenProteinSet: Training data for structural biology at scale
Multiple sequence alignments (MSAs) of proteins encode rich biological information and
have been workhorses in bioinformatic methods for tasks like protein design and protein …
have been workhorses in bioinformatic methods for tasks like protein design and protein …
A method for multiple-sequence-alignment-free protein structure prediction using a protein language model
Protein structure prediction pipelines based on artificial intelligence, such as AlphaFold2,
have achieved near-experimental accuracy. These advanced pipelines mainly rely on …
have achieved near-experimental accuracy. These advanced pipelines mainly rely on …
Current structure predictors are not learning the physics of protein folding
Motivation. Predicting the native state of a protein has long been considered a gateway
problem for understanding protein folding. Recent advances in structural modeling driven by …
problem for understanding protein folding. Recent advances in structural modeling driven by …
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) …
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data
Leveraging iterative alignment search through genomic and metagenome sequence
databases, we report the DeepMSA2 pipeline for uniform protein single-and multichain …
databases, we report the DeepMSA2 pipeline for uniform protein single-and multichain …
Helixfold-single: Msa-free protein structure prediction by using protein language model as an alternative
AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-
experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence …
experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence …
Protein language-model embeddings for fast, accurate, and alignment-free protein structure prediction
Advanced protein structure prediction requires evolutionary information from multiple
sequence alignments (MSAs) from evolutionary couplings that are not always available …
sequence alignments (MSAs) from evolutionary couplings that are not always available …
Single-sequence protein structure prediction using supervised transformer protein language models
Significant progress has been made in protein structure prediction in recent years. However,
it remains challenging for AlphaFold2 and other deep learning-based methods to predict …
it remains challenging for AlphaFold2 and other deep learning-based methods to predict …
[HTML][HTML] The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors
The function of proteins can often be inferred from their three-dimensional structures.
Experimental structural biologists spent decades studying these structures, but the …
Experimental structural biologists spent decades studying these structures, but the …