MOTIVATION: Automated machine learning (AutoML) solutions can bridge the gap between new computational advances and their real-world applications by enabling experimental scientists to build their own custom models. We examine different steps in the ...
SUMMARY: The vast majority of proteins still lack experimentally validated functional annotations, which highlights the importance of developing high-performance automated protein function prediction/annotation (AFP) methods. While existing approache...
MOTIVATION: Accurate quantitative information about protein abundance is crucial for understanding a biological system and its dynamics. Protein abundance is commonly estimated using label-free, bottom-up mass spectrometry (MS) protocols. Here, prote...
Protein science : a publication of the Protein Society
Sep 1, 2024
Disulfide bonds, covalently formed by sulfur atoms in cysteine residues, play a crucial role in protein folding and structure stability. Considering their significance, artificial disulfide bonds are often introduced to enhance protein thermostabilit...
Through iterative rounds of mutation and selection, proteins can be engineered to enhance their desired biological functions. Nevertheless, identifying optimal mutation sites for directed evolution remains challenging due to the vastness of the prote...
Cancer is a severe illness that significantly threatens human life and health. Anticancer peptides (ACPs) represent a promising therapeutic strategy for combating cancer. In silico methods enable rapid and accurate identification of ACPs without exte...
An overwhelming majority of protein-protein interaction (PPI) studies are conducted in a select few model organisms largely due to constraints in time and cost of the associated 'wet lab' experiments. In silico PPI inference methods are ideal tools t...
Protein science : a publication of the Protein Society
Jul 1, 2024
Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic of intense research. Capitalizing on the vast collection of protein structure predictions offered by AlphaFold (A...
UNLABELLED: Automated protein function prediction is a crucial and widely studied problem in bioinformatics. Computationally, protein function is a multilabel classification problem where only positive samples are defined and there is a large number ...
Database : the journal of biological databases and curation
Jun 7, 2024
The adaptive immune response plays a vital role in eliminating infected and aberrant cells from the body. This process hinges on the presentation of short peptides by major histocompatibility complex Class I molecules on the cell surface. Immunopepti...
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