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PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
Srinivasa M Gopal1, Shayantani Mukherjee, Yi-Ming Cheng
1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
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.
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