Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy

Min Li, Bing Teng, Wen Cai Lu, John Zeng Hui Zhang

Research output: Contribution to journalArticle

Abstract

Coarse-grained (CG) model has been a powerful tool in bridging the gap between theoretical studies and experimental phenomena in biological computing field. The reconstruction from a CG model to an atomic-detail structure is especially important in CG studies of biological systems. In this work, a rigid-fragment- and local-frame-based (RF-LF) backmapping method was proposed to achieve reverse mapping from CG models to atomic-level structures. The initial atomic-level structures were further refined to yield the final backmapping ones. With the popular Martini force field, the performance of the RF-LF method was extensively examined in the CG → AA (CG to AA) backmapping of protein/DNA/RNA systems. Besides, the RF-LF method was also extended to the backmapping of the TMFF model. Numerical results illustrate that the RF-LF backmapping method is generic and parameter-free and can provide a promising way to tackle atomic-level studies in CG models.

Original languageEnglish (US)
Article number31
JournalJournal of Molecular Modeling
Volume26
Issue number2
DOIs
StatePublished - Feb 1 2020

Keywords

  • CG → AA backmapping
  • Coarse-grained model
  • Local frame
  • Martini force field

ASJC Scopus subject areas

  • Catalysis
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Computational Theory and Mathematics
  • Inorganic Chemistry

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