Conformational analysis of nucleic acids revisited: Curves+

By Richard Lavery, Maher Moakher, John H. Maddocks, Daiva Petkeviciute, Krystyna Zakrzewska. Nucleic Acids Research, 2009

727 citations recorded by the source corpus.

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4c22d96a5bdc80542ef650ee5d2ea34dee250210

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Citations in the corpus

Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures (2019, background): “Other web servers for nucleic acid structures include the Curves+ web server (15) for analysis, 3DDART (16), and the ‘make-na’ server (10), built on top of NAB, for modeling (Supplemental Data S5).”
Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions (2014, background): “Encounter with the cognate sequence triggers a cooperative conversion of the non-specific to the specific complex and couples sequence recognition to catalytic cleavage [95] The DNA bound by HindIII is slightly bent by about 26° in comparison to ideal B-DNA [96] (calculated with the program CURVES [”