Evidence map›Paper›PMID 31965325›Full record

ArticleJournal of molecular modeling2020

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

Min Li, Bing Teng, WenCai Lu, John ZengHui Zhang

Abstract read
PubMed Publisher
In one paragraph

Article in Journal of molecular modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Min LiCollege of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China. limin122342@163.com.ORCID http://orcid.org/0000-0003-4442-4465
Bing TengCollege of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China.
WenCai LuCollege of Physics, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China.
John ZengHui ZhangSchool of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, People's Republic of China. john.zhang@nyu.edu.

Funding

China Postdoctoral Science Foundation 2018M630746National Natural Science Foundation of China 11847223National Natural Science Foundation of China 21803034Natural Science Foundation of Shandong Province ZR2019BB013
6 · The paper itself

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.

Indexed as

Molecular Dynamics SimulationDNAProteinsRNADNAProteinsRNACG → AA backmappingCoarse-grained modelLocal frameMartini force field

Identifiers

PMID31965325

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.