[HTML][HTML] Transformer-based deep learning for predicting protein properties in the life sciences
Recent developments in deep learning, coupled with an increasing number of sequenced
proteins, have led to a breakthrough in life science applications, in particular in protein …
proteins, have led to a breakthrough in life science applications, in particular in protein …
[HTML][HTML] On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins
K Lindorff-Larsen, BB Kragelund - Journal of Molecular Biology, 2021 - Elsevier
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and
many diverging properties. IDPs—and intrinsically disordered regions (IDRs) interspersed …
many diverging properties. IDPs—and intrinsically disordered regions (IDRs) interspersed …
Protein complex prediction with AlphaFold-Multimer
While the vast majority of well-structured single protein chains can now be predicted to high
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes …
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes …
[HTML][HTML] 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 …
[HTML][HTML] 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 …
[HTML][HTML] Using AlphaFold to predict the impact of single mutations on protein stability and function
MA Pak, KA Markhieva, MS Novikova, DS Petrov… - Plos one, 2023 - journals.plos.org
AlphaFold changed the field of structural biology by achieving three-dimensional (3D)
structure prediction from protein sequence at experimental quality. The astounding success …
structure prediction from protein sequence at experimental quality. The astounding success …
[PDF][PDF] Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure
Intrinsically disordered proteins and protein regions make up a substantial fraction of many
proteomes in which they play a wide variety of essential roles. A critical first step in …
proteomes in which they play a wide variety of essential roles. A critical first step in …
[HTML][HTML] Improving peptide-protein docking with AlphaFold-Multimer using forced sampling
I Johansson-Åkhe, B Wallner - Frontiers in bioinformatics, 2022 - frontiersin.org
Protein interactions are key in vital biological process. In many cases, particularly in
regulation, this interaction is between a protein and a shorter peptide fragment. Such …
regulation, this interaction is between a protein and a shorter peptide fragment. Such …
[HTML][HTML] AF2Complex predicts direct physical interactions in multimeric proteins with deep learning
Accurate descriptions of protein-protein interactions are essential for understanding
biological systems. Remarkably accurate atomic structures have been recently computed for …
biological systems. Remarkably accurate atomic structures have been recently computed for …
Protein–protein contact prediction by geometric triangle-aware protein language models
Abstract Information regarding the residue–residue distance between interacting proteins is
important for modelling the structures of protein complexes, as well as being valuable for …
important for modelling the structures of protein complexes, as well as being valuable for …