Paper Citing NAMD - Abstract
Gorska, Anna; Jasinski, Maciej; Trylska, Joanna
MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids
NUCLEIC ACIDS RESEARCH, 43 Art. No. e114, SEP 30 2015
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 (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 determines the hydrogen bonding network resolving the base pairing patterns, identifies secondary structure motifs (helices, junctions, loops, etc.) and pseudoknots. also estimates the energy of stacking and phosphate anion-base interactions. For many conformations, as in a molecular dynamics trajectory, provides averages of the above structural and energetic features and their evolution. We show functionality based on all-atom explicit solvent molecular dynamics trajectory of the 30S ribosomal subunit.
