Proteins play a vital role in various biological processes and achieve their functions through protein-protein interactions (PPIs). Thus, accurate identification of PPI sites is essential. Traditional biological methods for identifying PPIs are costl...
International journal of molecular sciences
Apr 28, 2024
The molecular weight (MW) of an enzyme is a critical parameter in enzyme-constrained models (ecModels). It is determined by two factors: the presence of subunits and the abundance of each subunit. Although the number of subunits (NS) can potentially ...
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...
Journal of molecular graphics & modelling
Apr 17, 2024
This study delves into the prediction of protein-peptide interactions using advanced machine learning techniques, comparing models such as sequence-based, standard CNNs, and traditional classifiers. Leveraging pre-trained language models and multi-vi...
Interdisciplinary sciences, computational life sciences
Apr 3, 2024
With the rapid development of NGS technology, the number of protein sequences has increased exponentially. Computational methods have been introduced in protein functional studies because the analysis of large numbers of proteins through biological e...
With advances in protein structure prediction thanks to deep learning models like AlphaFold, RNA structure prediction has recently received increased attention from deep learning researchers. RNAs introduce substantial challenges due to the sparser a...
N-terminal acetylation is one of the most common and important post-translational modifications (PTM) of eukaryotic proteins. PTM plays a crucial role in various cellular processes and disease pathogenesis. Thus, the accurate identification of N-term...
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 ...
Protein missense mutations and resulting protein stability changes are important causes for many human genetic diseases. However, the accurate prediction of stability changes due to mutations remains a challenging problem. To address this problem, we...
Protein-DNA and protein-RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are related to many human diseases. To understand the molecular mechanism of protein-DNA binding and protein-RNA b...
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