Since MD trajectories now typically produce tens of thousands of conformational snapshots it is necessary to be able to analyse such large datasets quickly. Curves+ can read MD trajectory files directly without the need for creating PDB format files. It currently deals with AMBER format trajectory files. It could be adapted to other formats, but it is also relatively easy to modify trajectory files to the AMBER format (see, for example, Simulaid by M. Mezei http://atlas.physbio.mssm.edu/∼mezei/simulaid/ or CatDCD by J. Gullingsrud http://www.ks.uiuc.edu/Development/MDTools/catdcd/ ).
Curves+ can be used to pick out and analyse a single snapshot or to analyse snapshots at chosen time intervals for the whole trajectory or extract information on a given sequence fragment from an ensemble of trajectories. The present version of Curves+ can analyse roughly 100 conformational snapshots of a 20-bp double-stranded DNA oligomer per second on a 2.5 GHz processor. When multiple snapshots are treated, printed output is suppressed and the program creates an unformatted file which can be treated with a supplementary program named Canal (Curves+ analysis). This program calculates the maxima, minima, mean and standard deviations of any chosen conformational parameters which are output in a list file. It can also generate time series and histograms which are output in flat files that can be used for producing graphics and will optionally calculate linear correlation coefficients between all helical, backbone and groove parameters, which can again be output in files for checking correlations graphically. The simple format of all files output by Canal makes them useable in any common graphic program. We have used both Gnuplot and MatLab (Mathworks Inc.) in preparing the illustrations of Canal data for this article. Canal can lastly be applied to the analysis of files produced by Curves+ from single structures. In this case, it can be used to plot the variation of chosen parameters along an oligomer or, as with trajectories, to look at parameter distributions and correlations. The use of Canal will be further illustrated in an article (manuscript in preparation) concerning the analysis of multiple MD trajectories from the ABC dataset (40 (link),41 (link)). A full user guide for Canal is available at the web site cited below.
Curves+ can be used to pick out and analyse a single snapshot or to analyse snapshots at chosen time intervals for the whole trajectory or extract information on a given sequence fragment from an ensemble of trajectories. The present version of Curves+ can analyse roughly 100 conformational snapshots of a 20-bp double-stranded DNA oligomer per second on a 2.5 GHz processor. When multiple snapshots are treated, printed output is suppressed and the program creates an unformatted file which can be treated with a supplementary program named Canal (Curves+ analysis). This program calculates the maxima, minima, mean and standard deviations of any chosen conformational parameters which are output in a list file. It can also generate time series and histograms which are output in flat files that can be used for producing graphics and will optionally calculate linear correlation coefficients between all helical, backbone and groove parameters, which can again be output in files for checking correlations graphically. The simple format of all files output by Canal makes them useable in any common graphic program. We have used both Gnuplot and MatLab (Mathworks Inc.) in preparing the illustrations of Canal data for this article. Canal can lastly be applied to the analysis of files produced by Curves+ from single structures. In this case, it can be used to plot the variation of chosen parameters along an oligomer or, as with trajectories, to look at parameter distributions and correlations. The use of Canal will be further illustrated in an article (manuscript in preparation) concerning the analysis of multiple MD trajectories from the ABC dataset (40 (link),41 (link)). A full user guide for Canal is available at the web site cited below.
