The remarkable recent advances in protein structure prediction have enabled computational modeling of protein structures with considerably higher accuracy than ever before. While state-of-the-art structure prediction methods provide self-assessment c...
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...
Protein is the most important component in organisms and plays an indispensable role in life activities. In recent years, a large number of intelligent methods have been proposed to predict protein function. These methods obtain different types of pr...
Exploiting sequence-structure-function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec...
A comprehensive understanding of protein functions holds significant promise for disease research and drug development, and proteins with analogous tertiary structures tend to exhibit similar functions. Protein fold recognition stands as a classical ...
Unlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins are lacking, hindering the utility of proteomics in applications where the sequences are unknown including variant calling, neoepitope identification, and metaproteo...
MOTIVATION: Deep-learning models are transforming biological research, including many bioinformatics and comparative genomics algorithms, such as sequence alignments, phylogenetic tree inference, and automatic classification of protein functions. Amo...
Protein sequence design can provide valuable insights into biopharmaceuticals and disease treatments. Currently, most protein sequence design methods based on deep learning focus on network architecture optimization, while ignoring protein-specific p...
IEEE journal of biomedical and health informatics
38483806
Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular me...
IEEE journal of biomedical and health informatics
37792659
In the Internet of Medical Things (IoMT), de novo peptide sequencing prediction is one of the most important techniques for the fields of disease prediction, diagnosis, and treatment. Recently, deep-learning-based peptide sequencing prediction has be...