An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modeling
Proteins are important ingredients in food and feed, they are the active components of many pharmaceutical products, and they are necessary, in the form of enzymes, for the success of many technical processes. However, production can be challenging, especially when using heterologous host cells such...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023002064 |
| _version_ | 1797384086078095360 |
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| author | J. Emonts J.F. Buyel |
| author_facet | J. Emonts J.F. Buyel |
| author_sort | J. Emonts |
| collection | DOAJ |
| description | Proteins are important ingredients in food and feed, they are the active components of many pharmaceutical products, and they are necessary, in the form of enzymes, for the success of many technical processes. However, production can be challenging, especially when using heterologous host cells such as bacteria to express and assemble recombinant mammalian proteins. The manufacturability of proteins can be hindered by low solubility, a tendency to aggregate, or inefficient purification. Tools such as in silico protein engineering and models that predict separation criteria can overcome these issues but usually require the complex shape and surface properties of proteins to be represented by a small number of quantitative numeric values known as descriptors, as similarly used to capture the features of small molecules. Here, we review the current status of protein descriptors, especially for application in quantitative structure activity relationship (QSAR) models. First, we describe the complexity of proteins and the properties that descriptors must accommodate. Then we introduce descriptors of shape and surface properties that quantify the global and local features of proteins. Finally, we highlight the current limitations of protein descriptors and propose strategies for the derivation of novel protein descriptors that are more informative. |
| first_indexed | 2024-03-08T21:30:25Z |
| format | Article |
| id | doaj.art-b8e249124b63439fa7ba236080c50650 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:30:25Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-b8e249124b63439fa7ba236080c506502023-12-21T07:31:35ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012132343247An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modelingJ. Emonts0J.F. Buyel1Fraunhofer Institute for Molecular Biology and Applied Ecology IME, GermanyUniversity of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Muthgasse 18, 1190 Vienna, Austria; Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, 52074 Aachen, Germany; Corresponding author at: University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Muthgasse 18, 1190 Vienna, Austria.Proteins are important ingredients in food and feed, they are the active components of many pharmaceutical products, and they are necessary, in the form of enzymes, for the success of many technical processes. However, production can be challenging, especially when using heterologous host cells such as bacteria to express and assemble recombinant mammalian proteins. The manufacturability of proteins can be hindered by low solubility, a tendency to aggregate, or inefficient purification. Tools such as in silico protein engineering and models that predict separation criteria can overcome these issues but usually require the complex shape and surface properties of proteins to be represented by a small number of quantitative numeric values known as descriptors, as similarly used to capture the features of small molecules. Here, we review the current status of protein descriptors, especially for application in quantitative structure activity relationship (QSAR) models. First, we describe the complexity of proteins and the properties that descriptors must accommodate. Then we introduce descriptors of shape and surface properties that quantify the global and local features of proteins. Finally, we highlight the current limitations of protein descriptors and propose strategies for the derivation of novel protein descriptors that are more informative.http://www.sciencedirect.com/science/article/pii/S2001037023002064Prediction of molecular featuresProtein structure complexityQuantitative structure activity relationshipScalar parametersShape and surface properties |
| spellingShingle | J. Emonts J.F. Buyel An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modeling Computational and Structural Biotechnology Journal Prediction of molecular features Protein structure complexity Quantitative structure activity relationship Scalar parameters Shape and surface properties |
| title | An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modeling |
| title_full | An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modeling |
| title_fullStr | An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modeling |
| title_full_unstemmed | An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modeling |
| title_short | An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modeling |
| title_sort | overview of descriptors to capture protein properties tools and perspectives in the context of qsar modeling |
| topic | Prediction of molecular features Protein structure complexity Quantitative structure activity relationship Scalar parameters Shape and surface properties |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023002064 |
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