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Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions

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Bioinformatics Research and Applications (ISBRA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9096))

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Abstract

Electron cryomicroscopy is an experimental technique that is capable to produce three dimensional gray-scale images for protein molecules, called density maps. At medium resolution, the atomic details of the molecule cannot be visualized from density maps. However, some features of the molecule can be seen such as the locations of major secondary structures and the skeleton of the molecule. In addition, the order and direction of the detected secondary structure traces can be inferred. We introduce a method to construct the entire model of a protein directly for traces extracted from the density map. The initial results show that this method has good potential. A single model was built for each of the 12 proteins used in the test. The RMSD100 of the models is slightly improved from our previous method.

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Authors and Affiliations

  1. Department of Computer Science, Tennessee State University, Nashville, TN, 37209, USA

    Kamal Al Nasr & Jing He

  2. Department of Computer Science, Old Dominion University, Norfolk, VA, 23529, USA

    Kamal Al Nasr & Jing He

Authors
  1. Kamal Al Nasr
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  2. Jing He
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Correspondence to Kamal Al Nasr .

Editor information

Editors and Affiliations

  1. Georgia State University, Atlanta, USA

    Robert Harrison

  2. Old Dominion University, Norfolk, USA

    Yaohang Li

  3. University of Connecticut, Storrs, Connecticut, USA

    Ion Măndoiu

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Nasr, K.A., He, J. (2015). Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions. In: Harrison, R., Li, Y., Măndoiu, I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science(), vol 9096. Springer, Cham. https://doi.org/10.1007/978-3-319-19048-8_1

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  • DOI: https://doi.org/10.1007/978-3-319-19048-8_1

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19047-1

  • Online ISBN: 978-3-319-19048-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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