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Nucleic Acids Res. 2015 Sep 30;43(17):e114. doi: 10.1093/nar/gkv559. Epub 2015 May 29.

MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids.

Author information

1
Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland Master studies at the Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, Warsaw, Poland.
2
Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland.
3
Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland joanna@cent.uw.edu.pl.

Abstract

Structural biology experiments and structure prediction tools have provided many high-resolution three-dimensional structures of nucleic acids. Also, molecular dynamics force field parameters have been adapted to simulating charged and flexible nucleic acid structures on microsecond time scales. Therefore, we can generate the dynamics of DNA or RNA molecules, but we still lack adequate tools for the analysis of the resulting huge amounts of data. We present MINT (Motif Identifier for Nucleic acids Trajectory) - an automatic tool for analyzing three-dimensional structures of RNA and DNA, and their full-atom molecular dynamics trajectories or other conformation sets (e.g. X-ray or nuclear magnetic resonance-derived structures). For each RNA or DNA conformation MINT determines the hydrogen bonding network resolving the base pairing patterns, identifies secondary structure motifs (helices, junctions, loops, etc.) and pseudoknots. MINT also estimates the energy of stacking and phosphate anion-base interactions. For many conformations, as in a molecular dynamics trajectory, MINT provides averages of the above structural and energetic features and their evolution. We show MINT functionality based on all-atom explicit solvent molecular dynamics trajectory of the 30S ribosomal subunit.

PMID:
26024667
PMCID:
PMC4787793
DOI:
10.1093/nar/gkv559
[Indexed for MEDLINE]
Free PMC Article

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