The knowledge of protein-protein interaction sites (PPIs) is crucial for protein functional annotation. Here we address the problem focusing on the prediction of putative PPIs considering as input protein sequences. The issue is important given the h...
Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new m...
Enzyme function annotation is a fundamental challenge, and numerous computational tools have been developed. However, most of these tools cannot accurately predict functional annotations, such as enzyme commission (EC) number, for less-studied protei...
MOTIVATION: The rapid accumulation of high-throughput sequence data demands the development of effective and efficient data-driven computational methods to functionally annotate proteins. However, most current approaches used for functional annotatio...
MOTIVATION: Coiled-coil domains (CCD) are widespread in all organisms and perform several crucial functions. Given their relevance, the computational detection of CCD is very important for protein functional annotation. State-of-the-art prediction me...
Protein function annotation is one of the most important research topics for revealing the essence of life at molecular level in the post-genome era. Current research shows that integrating multisource data can effectively improve the performance of ...
We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database. These models cover nearly all proteins that are known, including thos...
Functional annotation of open reading frames in microbial genomes remains substantially incomplete. Enzymes constitute the most prevalent functional gene class in microbial genomes and can be described by their specific catalytic functions using the ...
Accurate cell type annotation in single-cell RNA-sequencing data is essential for advancing biological and medical research, particularly in understanding disease progression and tumor microenvironments. However, existing methods are constrained by s...
Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of GO famili...