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

Proteins. 2010 Apr;78(5):1266-81. doi: 10.1002/prot.22645.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Computer Simulation*
  • Models, Molecular*
  • Molecular Structure
  • Nucleic Acid Conformation*
  • Nucleic Acids / chemistry*
  • Nucleic Acids / metabolism
  • Protein Conformation*
  • Protein Interaction Mapping / methods
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism
  • Software


  • Nucleic Acids
  • Proteins