The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI)...
DNA-binding and RNA-binding proteins are essential to an organism's normal life cycle. These proteins have diverse functions in various biological processes. DNA-binding proteins are crucial for DNA replication, transcription, repair, packaging, and ...
Small proteins (SPs) are a unique group of proteins that play crucial roles in many important biological processes. Exploring the biological function of SPs is necessary. In this study, the InterPro tool and the maximum correlation method were utiliz...
In shotgun proteomics, the proteome search engine analyzes mass spectra obtained by experiments, and then a peptide-spectra match (PSM) is reported for each spectrum. However, most of the PSMs identified are incorrect, and therefore various postproce...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 25, 2023
The advancements in next-generation sequencing technologies have given rise to large-scale, open-source protein databases consisting of hundreds of millions of sequences. However, to make these sequences useful in biomedical applications, they need t...
Protein structure analysis is essential in various bioinformatics domains such as drug discovery, disease diagnosis, and evolutionary studies. Within structural biology, the classification of protein structures is pivotal, employing machine learning ...
Journal of biomolecular structure & dynamics
Nov 18, 2023
Hormone-binding proteins (HBPs) are soluble carrier proteins that play a vital role in the growth and development of living organisms. Identifying HBPs accurately is crucial for understanding their functions. However, traditional wet lab experimental...
Spectral libraries are useful resources in proteomic data analysis. Recent advances in deep learning allow tandem mass spectra of peptides to be predicted from their amino acid sequences. This enables predicted spectral libraries to be compiled, and ...
Proteins are molecular machinery that participate in virtually all essential biological functions within the cell, which are tightly related to their 3D structure. The importance of understanding protein structure-function relationship is highlighted...
Genomics, proteomics & bioinformatics
Oct 19, 2023
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that...