Python toolkit for DNA geometry analysis and modelingстатьяТезисы
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Дата последнего поиска статьи во внешних источниках: 4 мая 2020 г.
Аннотация:The structure of DNA largely determines its function and affects the degree of chromatin compactization. With the development of new experimental techniques, an increasing number of struc- tures of macromolecules containing DNA become available. Modern computational methods allow us to obtain the molecular dynamics trajectories of macromolecules that exceed tens of microseconds. This new data can be analyzed with a number of state of the art software packages for DNA geometry analysis. However, the growth of data volumes requires the adaptation of well-established tools and the development of new tools for data processing. On the other hand, in order to achieve reproducible research, the data processing toolchain must be openly accessible, including the source codes of the libraries and executable files. We developed a set of tools for the rapid and high throughput analysis of DNA structures. This toolkit is written in Python with Numpy stack and MDAnalysis module for molecular struc- tures handling. Thus it is easily extensible and can open source by design. The current version of the software can be used for DNA molecular dynamics simulations analysis in a streamlined workflow. The developed software module also contains visual- ization tools for internal parameters of DNA geometry (such as reference frames and base-pair step parameters). Besides the anal- ysis, software is able to create molecular models of DNA geome- try. It is capable of homology modeling of DNA structure and assessment of DNA bending energy. The latter, coupled with a set of external geometric restraints, can be used to produce molecular models of complex DNA molecules. Overall the devel- oped software simplifies and accelerates the process of DNA geometry analysis. This work was supported by the Russian Science Foundation Grant No. 18-74-10006.