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Yoo, Je Joong
복잡계 자기조립 연구단
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Molecular dynamics simulations of DNA–DNA and DNA–protein interactions

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Title
Molecular dynamics simulations of DNA–DNA and DNA–protein interactions
Author(s)
Jejoong Yoo; David Winogradoff; Aleksei Aksimentiev
Subject
AMBER FORCE-FIELD, ; NUCLEIC-ACIDS, ; RNA, ; PARAMETERIZATION, ; NUCLEOSOME, ; PEPTIDES, ; ACCURACY, ; IMPROVES, ; BINDING, ; CHARMM
Publication Date
2020-10
Journal
CURRENT OPINION IN STRUCTURAL BIOLOGY, v.64, pp.88 - 96
Publisher
ELSEVIER B.V.
Abstract
© 2020 Elsevier Ltd. The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA–protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest
URI
https://pr.ibs.re.kr/handle/8788114/7618
DOI
10.1016/j.sbi.2020.06.007
ISSN
0959-440X
Appears in Collections:
Center for Self-assembly and Complexity(복잡계 자기조립 연구단) > 1. Journal Papers (저널논문)
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