do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations

The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations. It extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visualize statistical analyses of complex data obtained from the trajectories.

[1]  Alexander D. MacKerell,et al.  Molecular dynamics simulations of nucleic acid-protein complexes. , 2008, Current opinion in structural biology.

[2]  Karolin Luger,et al.  Nucleosome structure(s) and stability: variations on a theme. , 2011, Annual review of biophysics.

[3]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[4]  Xiang-Jun Lu,et al.  3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures , 2008, Nature Protocols.

[5]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[6]  W. Olson,et al.  3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. , 2003, Nucleic acids research.

[7]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[8]  David A Case,et al.  Twenty-five years of nucleic acid simulations. , 2013, Biopolymers.

[9]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[10]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

[11]  Hisao Masai,et al.  Eukaryotic chromosome DNA replication: where, when, and how? , 2010, Annual review of biochemistry.

[12]  Jayasha Shandilya,et al.  The transcription cycle in eukaryotes: from productive initiation to RNA polymerase II recycling. , 2012, Biochimica et biophysica acta.

[13]  S. Casjens.  The DNA-packaging nanomotor of tailed bacteriophages , 2011, Nature Reviews Microbiology.

[14]  J. H. Maddocks,et al.  Conformational analysis of nucleic acids revisited: Curves+ , 2009, Nucleic acids research.

[15]  B. Honig,et al.  Nuance in the double-helix and its role in protein-DNA recognition. , 2009, Current opinion in structural biology.

[16]  Christophe Blanchet,et al.  CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures , 2011, Nucleic Acids Res..

[17]  Estelle Crozat,et al.  FtsK DNA Translocase: The Fast Motor That Knows Where It's Going , 2010, Chembiochem : a European journal of chemical biology.