Current opinion in structural biology
Jun 13, 2023
Recent breakthroughs in protein structure prediction have increasingly relied on the use of deep neural networks. These recent methods are notable in that they produce 3-D atomic coordinates as a direct output of the networks, a feature which present...
The core of large-scale drug virtual screening is to select the binders accurately and efficiently with high affinity from large libraries of small molecules in which non-binders are usually dominant. The binding affinity is significantly influenced ...
Journal of chemical information and modeling
Jun 9, 2023
Protein kinases are a protein family that plays an important role in several complex diseases such as cancer and cardiovascular and immunological diseases. Protein kinases have conserved ATP binding sites, which when targeted can lead to similar acti...
International journal of biological macromolecules
Jun 6, 2023
Protein phosphorylation, catalyzed by kinases, is an important biochemical process, which plays an essential role in multiple cell signaling pathways. Meanwhile, protein-protein interactions (PPI) constitute the signaling pathways. Abnormal phosphory...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2023
Protein function prediction is a major challenge in the field of bioinformatics which aims at predicting the functions performed by a known protein. Many protein data forms like protein sequences, protein structures, protein-protein interaction netwo...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2023
The short-and-long range interactions amongst amino-acids in a protein sequence are primarily responsible for the function performed by the protein. Recently convolutional neural network (CNN)s have produced promising results on sequential data inclu...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2023
The intermolecular interactions between proteins and ligands occur through site-specific amino acid residues in the proteins, and the identification of these key residues plays a critical role in both interpreting protein function and facilitating dr...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2023
The recognition of protein-protein interaction sites (PPIs) is beneficial for the interpretation of protein functions and the development of new drugs. Traditional biological experiments to identify PPI sites are expensive and inefficient, leading to...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2023
Exploring drug-protein interactions (DPIs) through computational methods can effectively reduce the workload and the cost of DPI identification. Previous works try to predict DPIs by integrating and analyzing the unique features of drugs and proteins...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2023
Recent advancements of artificial intelligence based on deep learning algorithms have made it possible to computationally predict compound-protein interaction (CPI) without conducting laboratory experiments. In this manuscript, we integrated a graph ...