PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

Authors

  • Srinivasa M. Gopal,

    1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
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  • Shayantani Mukherjee,

    1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
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  • Yi-Ming Cheng,

    1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
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  • Michael Feig

    Corresponding author
    1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
    2. Department of Chemistry, Michigan State University, East Lansing, Michigan
    • Department of Biochemistry and Molecular Biology, Department of Chemistry, Michigan State University, East Lansing, Michigan
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Abstract

The new coarse graining model PRIMO/PRIMONA for proteins and nucleic acids is proposed. This model combines one to several heavy atoms into coarse-grained sites that are chosen to allow an analytical, high-resolution reconstruction of all-atom models based on molecular bonding geometry constraints. The accuracy of proposed reconstruction method in terms of structure and energetics is tested and compared with other popular reconstruction methods for a variety of protein and nucleic acid test sets. Proteins 2010. © 2009 Wiley-Liss, Inc.

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