Abstract：
:In this article, we present a method for the enhanced molecular dynamics simulation of protein and DNA systems called potential of mean force (PMF)-enriched sampling. The method uses partitions derived from the potentials of mean force, which we determined from DNA and protein structures in the Protein Data Bank (PDB). We define a partition function from a set of PDB-derived PMFs, which efficiently compensates for the error introduced by the assumption of a homogeneous partition function from the PDB datasets. The bias based on the PDB-derived partitions is added in the form of a hybrid Hamiltonian using a renormalization method, which adds the PMF-enriched gradient to the system depending on a linear weighting factor and the underlying force field. We validated the method using simulations of dialanine, the folding of TrpCage, and the conformational sampling of the Dickerson⁻Drew DNA dodecamer. Our results show the potential for the PMF-enriched simulation technique to enrich the conformational space of biomolecules along their order parameters, while we also observe a considerable speed increase in the sampling by factors ranging from 13.1 to 82. The novel method can effectively be combined with enhanced sampling or coarse-graining methods to enrich conformational sampling with a partition derived from the PDB.
journal_name
Int J Mol Scijournal_title
International journal of molecular sciencesauthors
Peter EK,Cerny Jdoi
10.3390/ijms19113405subject
Has Abstractpub_date
2018-10-30 00:00:00issue
11issn
1422-0067pii
ijms19113405journal_volume
19pub_type
杂志文章abstract：:Oxidative stress and the resulting damage to DNA are inevitable consequence of endogenous physiological processes further amplified by cellular responses to environmental exposures. If left unrepaired, oxidative DNA lesions can block essential processes such as transcription and replication or can induce mutations. Em...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms20020364
更新日期：2019-01-16 00:00:00
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journal_title：International journal of molecular sciences
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
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更新日期：2020-07-24 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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更新日期：2017-09-22 00:00:00
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journal_title：International journal of molecular sciences
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journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
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journal_title：International journal of molecular sciences
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更新日期：2019-04-04 00:00:00
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journal_title：International journal of molecular sciences
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更新日期：2014-05-05 00:00:00
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journal_title：International journal of molecular sciences
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更新日期：2020-12-31 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
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更新日期：2013-12-31 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
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更新日期：2020-07-08 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
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更新日期：2020-10-05 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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更新日期：2018-09-23 00:00:00
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journal_title：International journal of molecular sciences
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更新日期：2020-01-09 00:00:00
abstract：:We would like to submit the following correction to the published paper [1], the reason for this action is that the data in Table 3 were reanalyzed by one more accurate statistic method: On page 12, the sentence of paragraph three "OR and 95% CI were calculated by limited backward-LR (likelihood ratio) logistic regres...
journal_title：International journal of molecular sciences
pub_type： 已发布勘误
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更新日期：2017-09-04 00:00:00
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journal_title：International journal of molecular sciences
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journal_title：International journal of molecular sciences
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更新日期：2020-06-22 00:00:00
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journal_title：International journal of molecular sciences
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journal_title：International journal of molecular sciences
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更新日期：2019-03-13 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章,meta分析
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更新日期：2019-01-10 00:00:00
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journal_title：International journal of molecular sciences
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更新日期：2017-10-23 00:00:00
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journal_title：International journal of molecular sciences
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journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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pub_type： 杂志文章,评审
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更新日期：2015-03-04 00:00:00
