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- A review on computational models for predicting protein solubility
- Teerapat Pimtawong, Jun Ren, Jingyu Lee, Hyang-Mi Lee, Dokyun Na
- J. Microbiol. 2025;63(1):e.2408001. Published online January 24, 2025
- DOI: https://doi.org/10.71150/jm.2408001
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Abstract
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Protein solubility is a critical factor in the production of recombinant proteins, which are widely used in various industries, including pharmaceuticals, diagnostics, and biotechnology. Predicting protein solubility remains a challenging task due to the complexity of protein structures and the multitude of factors influencing solubility. Recent advances in computational methods, particularly those based on machine learning, have provided powerful tools for predicting protein solubility, thereby reducing the need for extensive experimental trials. This review provides an overview of current computational approaches to predict protein solubility. We discuss the datasets, features, and algorithms employed in these models. The review aims to bridge the gap between computational predictions and experimental validations, fostering the development of more accurate and reliable solubility prediction models that can significantly enhance recombinant protein production.
Review
- Ammonia-oxidizing archaea in biological interactions
- Jong-Geol Kim , Khaled S. Gazi , Samuel Imisi Awala , Man-Young Jung , Sung-Keun Rhee
- J. Microbiol. 2021;59(3):298-310. Published online February 23, 2021
- DOI: https://doi.org/10.1007/s12275-021-1005-z
- 58 View
- 0 Download
- 14 Web of Science
- 15 Crossref
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Abstract
- The third domain Archaea was known to thrive in extreme or anoxic environments based on cultivation studies. Recent metagenomics- based approaches revealed a widespread abundance of archaea, including ammonia-oxidizing archaea (AOA) of Thaumarchaeota in non-extreme and oxic environments. AOA alter nitrogen species availability by mediating the first step of chemolithoautotrophic nitrification, ammonia oxidation to nitrite, and are important primary producers in ecosystems, which affects the distribution and activity of other organisms in ecosystems. Thus, information on the interactions of AOA with other cohabiting organisms is a crucial element in understanding nitrogen and carbon cycles in ecosystems as well as the functioning of whole ecosystems. AOA are self-nourishing, and thus interactions of AOA with other organisms can often be indirect and broad. Besides, there are possibilities of specific and obligate interactions. Mechanisms of interaction are often not clearly identified but only inferred due to limited knowledge on the interaction factors analyzed by current technologies. Here, we overviewed different types of AOA interactions with other cohabiting organisms, which contribute to understanding AOA functions in ecosystems.
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Citations
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