The UniProt database is a valuable resource for biocatalyst discovery, yet predicting enzymatic functions remains challenging, especially for low-similarity sequences. Identifying superior enzymes with enhanced catalytic properties is even harder. To...
Proteins often perform biological functions by forming complexes, thereby accurately predicting the structure of protein complexes is crucial to understanding and mastering their functions, as well as facilitating drug discovery. Protein monomeric st...
The accurate prediction of enzyme function is crucial for elucidating disease mechanisms and identifying drug targets. Nevertheless, existing enzyme commission (EC) number prediction methods are limited by database coverage and the depth of sequence ...
Computer methods and programs in biomedicine
Mar 30, 2025
BACKGROUND AND OBJECTIVE: Protein-protein interactions (PPIs) play the key roles in myriad biological processes, helping to understand the protein function and disease pathology. Identification of PPIs and their interaction types through wet experime...
Peptides are ubiquitous and important biomolecules that self-assemble into diverse structures. Although extensive research has explored the effects of chemical composition and exterior conditions on self-assembly, a systematic study consolidating the...
Binding proteins play a crucial role in biological systems by selectively interacting with specific molecules, such as DNA, RNA, or peptides, to regulate various cellular processes. Their ability to recognize and bind target molecules with high speci...
In this communication, we introduce a new structure-based affinity predictor for protein-protein complexes. This predictor, dubbed PCANN (Protein Complex Affinity by Neural Network), uses the ESM-2 language model to encode the information about prote...
Journal of chemical information and modeling
Mar 7, 2025
Proteins, as the fundamental macromolecules of life, play critical roles in various biological processes. Recent advancements in intelligent protein function prediction methods leverage sequences, structures, and biomedical literature data. Among the...
IEEE journal of biomedical and health informatics
Mar 6, 2025
Predicting G protein-coupled receptor (GPCR) -ligand binding affinity plays a crucial role in drug development. However, determining GPCR-ligand binding affinities is time-consuming and resource-intensive. Although many studies used data-driven metho...
International journal of biological macromolecules
Mar 5, 2025
Intrinsically disordered proteins (IDPs) or regions (IDRs) are widespread in proteomes, and involved in several important biological processes and implicated in many diseases. Many computational methods for IDR prediction are being developed to decre...
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