NuProPlot: nucleic acid and protein interaction analysis and plotting program

Acta Crystallographica. Section D, Biological Crystallography
Lagnajeet Pradhan, Hyun Joo Nam

Abstract

Growing numbers of protein and nucleic acid complex structures are being determined and deposited in the Protein Data Bank and the Nucleic Acid Database. With the increasing complexity of these structures, it is challenging to analyse and visualize the three-dimensional interactions. The currently available programs for such analysis and visualization are limited in their applications. They can only analyse a subset of protein-nucleic acid complexes and require multiple iterations before obtaining plots that are suitable for presentation. An interactive web-based program, NuProPlot (http://www.nuproplot.com), has been developed which can automatically identify hydrogen, electrostatic and van der Waals interactions between proteins and nucleic acids and generate a plot showing all of the interactions. Protein-DNA and protein-RNA interactions can be visualized in simple two-dimensional schematics. Interactive schematic drawing options allow selection of the plotted area and repositioning of the individual interactions for better legibility. NuProPlot is a fully automated and user-friendly program providing various custom options. NuProPlot represents a greatly improved option for analysis and presentation of protein-nucleic acid ...Continue Reading

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Aug 2, 2012·Biochemistry·Lagnajeet PradhanHyun-Joo Nam

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Citations

Mar 2, 2016·Biochemistry·Lagnajeet PradhanHyun-Joo Nam
Jul 11, 2020·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·Kristel BergIngar Leiros
Mar 28, 2019·Molecular Biology Reports·Abbasali EmamjomehAmir Khodavirdipour
Aug 29, 2019·ACS Omega·Shichang LiHyun-Joo Nam

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