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

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.

SUBMITTER: Gopal SM

PROVIDER: S-EPMC2822037 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature

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

Gopal Srinivasa M SM Mukherjee Shayantani S Cheng Yi-Ming YM Feig Michael M

Proteins 20100401 5

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 ...[more]

PMID: 19967787

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