The structures of metalloproteins are essential for comprehending their functions and interactions. The breakthrough of AlphaFold has made it possible to predict protein structures with experimental accuracy. However, the type of metal ion that a met...
Exploring protein-protein interaction sites (PPIS) is of significance to elucidating the intrinsic mechanisms of diverse biological processes. On this basis, recent studies have applied deep learning-based technologies to overcome the high cost of we...
Phosphorylation is a substantial posttranslational modification of proteins that refers to adding a phosphate group to the amino acid side chain after translation process in the ribosome. It is vital to coordinate cellular functions, such as regulati...
Protein-protein interactions (PPIs) play an essential role in life activities. Many artificial intelligence algorithms based on protein sequence information have been developed to predict PPIs. However, these models have difficulty dealing with vario...
We apply methods of Artificial Intelligence and Machine Learning to protein dynamic bioinformatics. We rewrite the sequences of a large protein data set, containing both folded and intrinsically disordered molecules, using a representation developed ...
Determining binding affinities in protein-protein and protein-peptide complexes is a challenging task that directly impacts the development of peptide and protein pharmaceuticals. Although several models have been proposed to predict the value of the...
This study introduces TooT-PLM-ionCT, a comprehensive framework that consolidates three distinct systems, each meticulously tailored for one of the following tasks: distinguishing ion channels (ICs) from membrane proteins (MPs), segregating ion trans...
During the last three decades, antimicrobial peptides (AMPs) have emerged as a promising therapeutic alternative to antibiotics. The approaches for designing AMPs span from experimental trial-and-error methods to synthetic hybrid peptide libraries. T...
Proteins are used in various biotechnological applications, often requiring the optimization of protein properties by introducing specific amino-acid exchanges. Deep mutational scanning (DMS) is an effective high-throughput method for evaluating the ...
Antibodies represent a crucial class of complex protein therapeutics and are essential in the treatment of a wide range of human diseases. Traditional antibody discovery methods, such as hybridoma and phage display technologies, suffer from limitatio...