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

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.

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Acknowledgments

We thank the Supercomputer Center of East China Normal University for providing us computer time.

Funding

This work was supported by the National Natural Science Foundation of China (Grant no. 21803034 and Grant no. 11847223), China Postdoctoral Science Foundation (Grant no. 2018 M630746), and Natural Science Foundation of Shandong Province (Grant no. ZR2019BB013).

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Correspondence to Min Li or John ZengHui Zhang.

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Li, M., Teng, B., Lu, W. et al. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. J Mol Model 26, 31 (2020). https://doi.org/10.1007/s00894-020-4298-7

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Keywords

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