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- W2513408641 abstract "Simulating the functional motions of biomolecular systems requires large computational resources. We introduce a computationally inexpensive protocol for the systematic testing of hypotheses regarding the dynamic behavior of proteins and nucleic acids. The protocol is based on natural move Monte Carlo, a highly efficient conformational sampling method with built-in customization capabilities that allows researchers to design and perform a large number of simulations to investigate functional motions in biological systems. We demonstrate the use of this protocol on both a protein and a DNA case study. Firstly, we investigate the plasticity of a class II major histocompatibility complex in the absence of a bound peptide. Secondly, we study the effects of the epigenetic mark 5-hydroxymethyl on cytosine on the structure of the Dickerson-Drew dodecamer. We show how our customized natural moves protocol can be used to investigate causal relationships of functional motions in biological systems." @default.
- W2513408641 created "2016-09-16" @default.
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- W2513408641 date "2016-08-01" @default.
- W2513408641 modified "2023-10-18" @default.
- W2513408641 title "Modeling Functional Motions of Biological Systems by Customized Natural Moves" @default.
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- W2513408641 doi "https://doi.org/10.1016/j.bpj.2016.06.028" @default.
- W2513408641 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/5002067" @default.
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