Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session I

18 – POS Board 18 Motif Identifier for Nucleic Acid Trajectory Anna Górska 1 , Maciej Jasinski 1 , Joanna Trylska 1 . 1 University of Warsaw, Warsaw, Poland, 2 University of Warsaw, Warsaw, Poland. Many of the structural and dynamic properties of RNA and RNA-protein complexes can be investigated using molecular dynamics or Monte Carlo simulations. However, this requires post- processing and analysis of trajectories containing large number of molecular conformations. While there are many tools for the analysis of single RNA conformations, only a few of them enable analyzing multiple RNA conformations. We present a software tool, Motif Identifier for Nucleic Acid Trajectory (MINT), for analyzing three-dimensional structures of RNA molecules, their full-atom molecular dynamics trajectories or other conformation sets (e.g. X-ray or NMR-derived structures). For each RNA conformation MINT determines the base pairing patterns, identifies secondary structure motifs (helices, triplexes, junctions, loops, bulges etc.) and pseudo-knots. Moreover, for stacked nucleotides the energy of interaction is calculated. If many conformations are analyzed, MINT provides average values of these parameters and description of their evolution. MINT is written in Python programming language. The analysis of molecular dynamics trajectories can be run in parallel using any number of CPUs, limited only by the amount of available memory. The main output consists of several .csv type files that can be opened in any spreadsheet application. Visualizations of 3D structures can be made in popular molecular viewers thanks to the provided set of .pdb files with the occupancy column replaced with the values of the investigated parameters (e.g., the number of hydrogen bonds that the atom takes part in). For 2D visualizations MINT provides an .html file that can be opened in the VARNA (http://varna.lri.fr/) applet and the .xml input file for the RNAMovies (http://bibiserv.techfak.uni- bielefeld.de/rnamovies/) program. MINT is a free software released under the terms of the GPLv2.0 license and available at http://www.mint.cent.edu.pl. The MINT package can be either downloaded or used as a webserver.

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