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Nature biotechnology
Feb 15, 2024
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New methods promise to escape the constraints of natural and laboratory evolution, accelera...
BMC bioinformatics
Jan 30, 2024
BACKGROUND: The Drug-Target Interaction (DTI) prediction uses a drug molecule and a protein sequence as inputs to predict the binding affinity value. In recent years, deep learning-based models have gotten more attention. These methods have two modul...
Proceedings of the National Academy of Sciences of the United States of America
Jan 29, 2024
Amino acid mutations that lower a protein's thermodynamic stability are implicated in numerous diseases, and engineered proteins with enhanced stability can be important in research and medicine. Computational methods for predicting how mutations per...
PloS one
Jan 29, 2024
Convolutional neural networks (CNNs) are currently among the most widely-used deep neural network (DNN) architectures available and achieve state-of-the-art performance for many problems. Originally applied to computer vision tasks, CNNs work well wi...
PLoS computational biology
Jan 19, 2024
One of the challenges in a viral pandemic is the emergence of novel variants with different phenotypical characteristics. An ability to forecast future viral individuals at the sequence level enables advance preparation by characterizing the sequence...
Interdisciplinary sciences, computational life sciences
Jan 11, 2024
The protein S-nitrosylation (SNO) is a significant post-translational modification that affects the stability, activity, cellular localization, and function of proteins. Therefore, highly accurate prediction of SNO sites aids in grasping biological f...
Journal of chemical theory and computation
Jan 11, 2024
With the ongoing development of peptide self-assembling materials, there is growing interest in exploring novel functional peptide sequences. From short peptides to long polypeptides, as the functionality increases, the sequence space is also expandi...
Applied microbiology and biotechnology
Jan 4, 2024
A complete catalase-encoding gene, designated soiCat1, was obtained from soil samples via metagenomic sequencing, assembly, and gene prediction. soiCat1 showed 73% identity to a catalase-encoding gene of Mucilaginibacter rubeus strain P1, and the ami...
Computers in biology and medicine
Jan 3, 2024
Protein mutations can significantly influence protein solubility, which results in altered protein functions and leads to various diseases. Despite tremendous effort, machine learning prediction of protein solubility changes upon mutation remains a c...
Computers in biology and medicine
Jan 3, 2024
Serine phosphorylation plays a pivotal role in the pathogenesis of various cellular processes and diseases. Roughly 81% of human diseases have links to phosphorylation, and an overwhelming 86.4% of protein phosphorylation takes place at serine residu...