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 …
Easy and accurate protein structure prediction using ColabFold
Since its public release in 2021, AlphaFold2 (AF2) has made investigating biological
questions, by using predicted protein structures of single monomers or full complexes, a …
questions, by using predicted protein structures of single monomers or full complexes, a …
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
AlphaFold2 revolutionized structural biology with the ability to predict protein structures with
exceptionally high accuracy. Its implementation, however, lacks the code and data required …
exceptionally high accuracy. Its implementation, however, lacks the code and data required …
{nnScaler}:{Constraint-Guided} Parallelization Plan Generation for Deep Learning Training
With the growing model size of deep neural networks (DNN), deep learning training is
increasingly relying on handcrafted search spaces to find efficient parallelization execution …
increasingly relying on handcrafted search spaces to find efficient parallelization execution …
Uni-Fold: an open-source platform for developing protein folding models beyond AlphaFold
Recent breakthroughs on protein structure prediction, namely AlphaFold, have led to
unprecedented new possibilities in related areas. However, the lack of training utilities in its …
unprecedented new possibilities in related areas. However, the lack of training utilities in its …
Structural biology at the scale of proteomes
N Bouatta, M AlQuraishi - Nature structural & molecular biology, 2023 - nature.com
AlphaFold2 has already changed structural biology, but its true power may lie in how it
changes the way we think about cells and organisms. Two studies broadly assess its utility …
changes the way we think about cells and organisms. Two studies broadly assess its utility …
Helixfold: An efficient implementation of alphafold2 using paddlepaddle
Accurate protein structure prediction can significantly accelerate the development of life
science. The accuracy of AlphaFold2, a frontier end-to-end structure prediction system, is …
science. The accuracy of AlphaFold2, a frontier end-to-end structure prediction system, is …
DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
Motivation Predicting protein structures with high accuracy is a critical challenge for the
broad community of life sciences and industry. Despite progress made by deep neural …
broad community of life sciences and industry. Despite progress made by deep neural …
Recent progress of protein tertiary structure prediction
The prediction of three-dimensional (3D) protein structure from amino acid sequences has
stood as a significant challenge in computational and structural bioinformatics for decades …
stood as a significant challenge in computational and structural bioinformatics for decades …
Dsp: Dynamic sequence parallelism for multi-dimensional transformers
Scaling multi-dimensional transformers to long sequences is indispensable across various
domains. However, the challenges of large memory requirements and slow speeds of such …
domains. However, the challenges of large memory requirements and slow speeds of such …