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PRIMO/PRIMONA: A coarse‐grained model for proteins and nucleic acids that preserves near‐atomistic accuracy
Author(s) -
Gopal Srinivasa M.,
Mukherjee Shayantani,
Cheng YiMing,
Feig Michael
Publication year - 2010
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22645
Subject(s) - nucleic acid , granularity , biological system , resolution (logic) , algorithm , computer science , chemistry , computational biology , biology , artificial intelligence , biochemistry , operating system
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.