Bioinformatics (Oxford, England)
Apr 28, 2022
MOTIVATION: Exploring drug-protein interactions (DPIs) provides a rapid and precise approach to assist in laboratory experiments for discovering new drugs. Network-based methods usually utilize a drug-protein association network and predict DPIs by t...
Bioinformatics (Oxford, England)
Apr 28, 2022
MOTIVATION: The development of microscopic imaging techniques enables us to study protein subcellular locations from the tissue level down to the cell level, contributing to the rapid development of image-based protein subcellular location prediction...
Bioinformatics (Oxford, England)
Apr 12, 2022
MOTIVATION: Graphs or networks are widely utilized to model the interactions between different entities (e.g. proteins, drugs, etc.) for biomedical applications. Predicting potential interactions/links in biomedical networks is important for understa...
Bioinformatics (Oxford, England)
Apr 12, 2022
MOTIVATION: Kinase-catalyzed phosphorylation of proteins forms the backbone of signal transduction within the cell, enabling the coordination of numerous processes such as the cell cycle, apoptosis, and differentiation. Although on the order of 105 p...
Bioinformatics (Oxford, England)
Apr 12, 2022
MOTIVATION: The interactions between proteins and other molecules are essential to many biological and cellular processes. Experimental identification of interface residues is a time-consuming, costly and challenging task, while protein sequence data...
Bioinformatics (Oxford, England)
Apr 12, 2022
SUMMARY: Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for t...
Structure (London, England : 1993)
Apr 7, 2022
Proteins, the building blocks of life, often form large assemblies to perform their function but are traditionally studied separately in structural biology. In this issue of Structure, Skalidis et al. (2022) present a workflow to identify members of ...
Bioinformatics (Oxford, England)
Mar 28, 2022
MOTIVATION: Cryo-electron microscopy (cryo-EM) is a widely used technology for ultrastructure determination, which constructs the 3D structures of protein and macromolecular complex from a set of 2D micrographs. However, limited by the electron beam ...
Bioinformatics (Oxford, England)
Mar 28, 2022
MOTIVATION: Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accur...
Bioinformatics (Oxford, England)
Mar 28, 2022
MOTIVATION: Protein model quality assessment is a key component of protein structure prediction. In recent research, the voxelization feature was used to characterize the local structural information of residues, but it may be insufficient for descri...