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 ...
BACKGROUND: Protein language models, inspired by the success of large language models in deciphering human language, have emerged as powerful tools for unraveling the intricate code of life inscribed within protein sequences. They have gained signifi...
Journal of chemical information and modeling
Mar 12, 2024
The protein-ligand binding free energy is a central quantity in structure-based computational drug discovery efforts. Although popular alchemical methods provide sound statistical means of computing the binding free energy of a large breadth of syste...
BACKGROUND: Predicting protein-protein interactions (PPIs) from sequence data is a key challenge in computational biology. While various computational methods have been proposed, the utilization of sequence embeddings from protein language models, wh...
Interdisciplinary sciences, computational life sciences
Mar 8, 2024
As one of the most important post-translational modifications (PTMs), protein phosphorylation plays a key role in a variety of biological processes. Many studies have shown that protein phosphorylation is associated with various human diseases. There...
Interdisciplinary sciences, computational life sciences
Mar 8, 2024
Accurately predicting compound-protein interactions (CPI) is a critical task in computer-aided drug design. In recent years, the exponential growth of compound activity and biomedical data has highlighted the need for efficient and interpretable pred...
Journal of chemical information and modeling
Mar 8, 2024
Predicting the protein-nucleic acid (PNA) binding affinity solely from their sequences is of paramount importance for the experimental design and analysis of PNA interactions (PNAIs). A large number of currently developed models for binding affinity ...
Proceedings of the National Academy of Sciences of the United States of America
Mar 7, 2024
Proteins are a diverse class of biomolecules responsible for wide-ranging cellular functions, from catalyzing reactions to recognizing pathogens. The ability to evolve proteins rapidly and inexpensively toward improved properties is a common objectiv...
Identifying binding compounds against a target protein is crucial for large-scale virtual screening in drug development. Recently, network-based methods have been developed for compound-protein interaction (CPI) prediction. However, they are difficul...
Protein-protein interactions (PPIs) involve the physical or functional contact between two or more proteins. Generally, proteins that can interact with each other always have special relationships. Some previous studies have reported that gene ontolo...
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