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analyze nucleic acid 3D structures and MD trajectories

Project description

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Introduction

Barnaba is a tool for analyzing RNA three-dimensional structures and simulations. Barnaba uses MDtraj to read/write topology and trajectory files, as such it supports several formats including pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop, and more. Barnaba has been developed by Sandro Bottaro with the crucial help of Giovanni Bussi, Giovanni Pinamonti, Sabine Rei{ss}er and Wouter Boomsma.

This is what you can do with Barnaba:

  1. Calculate eRMSD [1]
  2. Calculate RMSD after optimal alignment
  3. Search for single/double stranded RNA motifs in the PDB database or in simulations [1]
  4. Annotate PDB structures and trajectories with the Leontis-Westhof classification
  5. Produce dynamic secondary structure figures in SVG format
  6. Cluster nucleic acids structures using the eRMSD as a metric distance
  7. Calculate elastic network models for nucleic acids and nucleic acids/protein complexes [2]
  8. Calculate backbone and pucker torsion angles in a PDB structure or trajectory
  9. Back-calculate 3J scalar couplings from PDB structure or trajectory
  10. Score three-dimensional structures using eSCORE [1]

For bugs, questions or comments contact Sandro at sandro dot bottaro (guesswhat) gmail dot com

If you use Barnaba in your work, please cite the following paper:

@article{bottaro2019barnaba,
        title={Barnaba: software for analysis of nucleic acid structures and trajectories},
        author={Bottaro, Sandro and Bussi, Giovanni and Pinamonti, Giovanni and Rei{\ss}er, Sabine and Boomsma, Wouter and Lindorff-Larsen, Kresten},
        journal={RNA},
        volume={25},
        number={2},
        pages={219--231},
        year={2019},
        publisher={Cold Spring Harbor Lab}
}

The manuscript is also available on biorXiv here: https://www.biorxiv.org/content/10.1101/345678v3

Requirements

Barnaba requires:
  • Python 2.7.x or > 3.3
  • Numpy
  • Scipy
  • Mdtraj 1.9
  • future

Barnaba requires mdtraj (http://mdtraj.org/) for manipulating structures and trajectories. To perform cluster analysis, scikit-learn is required too.

Required packages can be installed using pip, e.g.:

pip install mdtraj

Installation

You can obtain the latest tagged version of barnaba using pip:

pip install barnaba

On MacOS, you can install the same tagged version using the python distributed with MacPorts:

sudo port install py36-barnaba

Just replace 36 with the python version that you prefer to use.

Alternatively, you can find the most recent version of barnaba on Github:

git clone git://github.com/srnas/barnaba.git

then move to the barnaba directory and run the command

pip install -e .

Notice that barnaba is installed using setuptools_scm that is not compatible with git archives. Thus, you would not be able to install barnaba from a git tarball.

Some users might experience issues installing MDtraj using pip. If this is the case, we recommend installing MDtraj using conda:

conda install –channel omnia mdtraj

Usage

Barnaba can be either used as a Python library or as a commandline tool. A number of Notebook examples can be found in the examples directory. The notebooks for conducting the analyses and producing the figures in the manuscript can be found in the folder manuscript_figures .

Alternatively, the command-line interface can be found in the bin directory. Here’s a minimal how-to

  1. minimal help: barnaba –help

  2. Calculate the ERMSD between structures

    barnaba ERMSD –ref ../test/data/sample1.pdb –pdb ../test/data/sample2.pdb

    trajectories can be provided as well, by specifying a topology file

    barnaba ERMSD –ref ../test/data/sample1.pdb –top ../test/data/sample1.pdb –trj ../test/data/samples.xtc

    other accepted options are shown in a function-specific help

    barnaba ERMSD –help

  3. Calculate the RMSD between structures

    barnaba RMSD –ref ../test/data/sample1.pdb –pdb ../test/data/sample2.pdb –dump

  4. Find single stranded motif

    barnaba SS_MOTIF –query ../test/data/GNRA.pdb –pdb ../test/data/1S72.pdb

  5. Find double stranded motif. l1 and l2 are the lengths of the two strands

    barnaba DS_MOTIF –query ../test/data/SARCIN.pdb –pdb ../test/data/1S72.pdb –l1 8 –l2 7

  6. Annotate structures/trajectories according to the Leontis/Westhof classification.

    barnaba ANNOTATE –pdb ../test/data/SARCIN.pdb

  7. Produce dynamic secondary-structure figures. It requires as input the files .pairing and .stacking produced with the ANNOTATE command.

    barnaba SEC_STRUCTURE –ann outfile.ANNOTATE.stacking.out outfile.ANNOTATE.pairing.out

  8. Calculate backbone/sugar/pseudorotation angles

    barnaba TORSION –pdb ../test/data/GNRA.pdb –backbone –sugar –pucker

  9. Calculate J-couplings

    barnaba JCOUPLING –pdb ../test/data/sample1.pdb

  10. Calculate elastic network models for RNA and predict SHAPE reactivity. NB: only works with PDB.

    barnaba ENM –pdb ../test/data/GNRA.pdb –shape

  11. Calculate relative positions between bases R_ij ang G vectors for pairs within ellipsoidal cutoff

barnaba DUMP –pdb ../test/data/GNRA.pdb –dumpG –dumpR
  1. Extract fragments from structures with a given sequence. NB: only works with PDB.

    barnaba SNIPPET –pdb ../test/data/1S72.pdb –seq NNGNRANN

  2. Calculate ESCORE

barnaba ESCORE –ff ../test/data/1S72.pdb –pdb ../test/data/sample1.pdb

References

[1] Bottaro, Sandro, Francesco Di Palma, and Giovanni Bussi.
“The role of nucleobase interactions in RNA structure and dynamics.” Nucleic acids research 42.21 (2014): 13306-13314.
[2] Pinamonti, Giovanni, et al.
“Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.” Nucleic acids research 43.15 (2015): 7260-7269.

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