PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy.
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.
Gopal
Srinivasa M
SM
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
Mukherjee
Shayantani
S
Cheng
Yi-Ming
YM
Feig
Michael
M
D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012984:Software
D009696:Nucleic Acids; D011506:Proteins