Short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry an...
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2 and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we show that, although these deep learning approaches have originally been develop...
The interaction between proteins and RNA is closely related to various human diseases. Computer-aided drug design can be facilitated by detecting the RNA sites that bind proteins. However, due to the aggregation of binding sites in RNA sequences, hig...
In biological systems, Glutamic acid is a crucial amino acid which is used in protein biosynthesis. Carboxylation of glutamic acid is a significant post-translational modification which plays important role in blood coagulation by activating prothrom...
Although thermal proteome profiling (TPP) acts as a popular modification-free approach for drug target deconvolution, some key problems are still limiting screening sensitivity. In the prevailing TPP workflow, only the soluble fractions are analyzed ...
MOTIVATION: Protein backbone angle prediction has achieved significant accuracy improvement with the development of deep learning methods. Usually the same deep learning model is used in making prediction for all residues regardless of the categories...
Journal of chemical information and modeling
Jan 3, 2022
Deep learning has been successfully applied to structure-based protein-ligand affinity prediction, yet the black box nature of these models raises some questions. In a previous study, we presented K, a convolutional neural network that predicted the ...
Characterization of protein complexes, i.e. sets of proteins assembling into a single larger physical entity, is important, as such assemblies play many essential roles in cells such as gene regulation. From networks of protein-protein interactions, ...
Current opinion in structural biology
Dec 25, 2021
Deep learning approaches have produced substantial breakthroughs in fields such as image classification and natural language processing and are making rapid inroads in the area of protein design. Many generative models of proteins have been developed...
Current opinion in structural biology
Dec 23, 2021
Proteins interact through their interfaces to fulfill essential functions in the cell. They bind to their partners in a highly specific manner and form complexes that have a profound effect on understanding the biological pathways they are involved i...