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3D-BMPP: 3D Beta-Barrel Membrane Protein Predictor

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Homology Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2627))

Abstract

β-barrel membrane proteins (βMPs), found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts, play important roles in membrane anchoring, pore formation, and enzyme activities. However, it is often difficult to determine their structures experimentally, and the knowledge of their structures is currently limited. We have developed a method to predict the 3D architectures of βMPs. We can accurately construct transmembrane domains of βMPs by predicting their strand registers, from which full 3D atomic structures are derived. Using 3D Beta-barrel Membrane Protein Predictor (3D-BMPP), we can further accurately model the extended beta barrels and loops in non-TM regions with overall greater structure prediction coverage. 3DBMPP is a general technique that can be applied to protein families with limited sequences as well as proteins with novel folds. Applications of 3DBMPP can be broadly applied to genome-wide βMPs structure prediction.

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Acknowledgments

This work is support by NIH grant R35 GM127084.

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Authors and Affiliations

  1. Center for Bioinformatics and Quantitative Biology and Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, USA

    Wei Tian, Meishan Lin, Ke Tang, Manisha Barse & Jie Liang

  2. Computational Biology Research Lab and Department of Computing, National University of Computer and Emerging Sciences, Islamabad, Pakistan

    Hammad Naveed

Authors
  1. Wei Tian
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  2. Meishan Lin
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  3. Ke Tang
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  4. Manisha Barse
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  5. Hammad Naveed
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  6. Jie Liang
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Corresponding authors

Correspondence to Hammad Naveed or Jie Liang .

Editor information

Editors and Affiliations

  1. Faculty of Chemistry, University of Warsaw, Warsaw, Poland

    Sławomir Filipek

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Tian, W., Lin, M., Tang, K., Barse, M., Naveed, H., Liang, J. (2023). 3D-BMPP: 3D Beta-Barrel Membrane Protein Predictor. In: Filipek, S. (eds) Homology Modeling. Methods in Molecular Biology, vol 2627. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2974-1_17

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  • DOI: https://doi.org/10.1007/978-1-0716-2974-1_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2973-4

  • Online ISBN: 978-1-0716-2974-1

  • eBook Packages: Springer Protocols

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