[HTML][HTML] Computational tools to predict context-specific protein complexes
Interactions between thousands of proteins define cells' protein–protein interaction (PPI)
network. Some of these interactions lead to the formation of protein complexes. It is …
network. Some of these interactions lead to the formation of protein complexes. It is …
Exploring structural diversity across the protein universe with The Encyclopedia of Domains
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted
protein structures composed of domains, which are independently folding units found in …
protein structures composed of domains, which are independently folding units found in …
Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes
Characterization of shared patterns of RNA expression between genes across conditions
has led to the discovery of regulatory networks and novel biological functions. However, it is …
has led to the discovery of regulatory networks and novel biological functions. However, it is …
Knots and θ-Curves Identification in Polymeric Chains and Native Proteins Using Neural Networks
F Bruno da Silva, B Gabrovšek, M Korpacz… - …, 2024 - ACS Publications
Entanglement in proteins is a fascinating structural motif that is neither easy to detect via
traditional methods nor fully understood. Recent advancements in AI-driven models have …
traditional methods nor fully understood. Recent advancements in AI-driven models have …
Knot or not? Identifying unknotted proteins in knotted families with sequence‐based Machine Learning model
Knotted proteins, although scarce, are crucial structural components of certain protein
families, and their roles continue to be a topic of intense research. Capitalizing on the vast …
families, and their roles continue to be a topic of intense research. Capitalizing on the vast …
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?
Understanding the conformational dynamics of proteins, such as the inward-facing (IF) and
outward-facing (OF) transition observed in transporters, is vital for elucidating their functional …
outward-facing (OF) transition observed in transporters, is vital for elucidating their functional …
Sequence‐Similar Protein Domain Pairs With Structural or Topological Dissimilarity
P Røgen - Proteins: Structure, Function, and Bioinformatics, 2024 - Wiley Online Library
For a variety of applications, protein structures are clustered by sequence similarity, and
sequence‐redundant structures are disregarded. Sequence‐similar chains are likely to have …
sequence‐redundant structures are disregarded. Sequence‐similar chains are likely to have …