backmap 0.0.3.post0.dev1

Shows protein backbone structures in compact graphical form using Ramachandran numbers

Contents

• 1   Introduction
• 2   Installation
  • 2.1   PIP Installation
  • 2.2   GIT Installation
• 3   Usage
  • 3.1   In-script usage
  • 3.2   Standalone usage
• 4   Examples
  • 4.1   Example 1: A stable protein (1xqq)
  • 4.2   Example 2: An intrinsically disordered protein (2fft)
• 5   Publications

1   Introduction

This tool provides easily readable “pictures” of protein conformations, ensembles, and trajectories saved as either a combined protein databank (PDB) structure file, or a directory of such files, and produces graphs.

2   Installation

2.1   PIP Installation

Running the following at command line would get the job done (the ‘-I’ is not necessary, but ensures the latest sub-version is installed):

$ pip install -I backmap

2.2   GIT Installation

$ git clone https://github.com/ranjanmannige/backmap.git
$ cd backmap
$ python setup.py install
$ python setup.py test

3   Usage

3.1   In-script usage

import backmap as bm
print bm.R(phi=0,psi=0)

For more information about module usage, refer to the manuscript associated with this module

3.2   Standalone usage

After installation, the following commands produce a variety of graphs (exampled below).

python -m backmap.__init__ -pdb ./pdbs/ProteinDatabankStructureFilename.pdb
python -m backmap.__init__ -pdb /directory/containing/pdbs/

The .__init__ is needed because the main file we are referencing is backmap/__init__.py.

4   Examples

4.1   Example 1: A stable protein (1xqq)

The Panels (b) through (f) were created by running the following command within thin the downloaded directory (Panel (a) was created using VMD.

python -m backmap.__init__ -pdb ./tests/pdbs/1xqq.pdb

As evident below, the graphs generated from the protein ensemble 1xqq describes a conformationally stable protein (each graph is detailed below).

Each column in Panel (b) describes the histogram in Ramachandran number (R) space for a single model/timeframe. These histograms show the presence of both helices (at R ~ 0.34) and sheets (at R ~ 0.52). Additionally, Panels (c) and (d) describe the per-residue conformational plots (colored by two different metrics or CMAPs), which show that most of the protein backbone remains relatively stable (e.g., few fluctuations in state or ‘color’ are evident over the frame #). Finally, Panel (e) describes the extent towards which a single residue’s state has deviated from the first frame, and Panel (f) describes the extent towards which a single residue’s state has deviated from its state in the previous frame. Both these graphs, as expected from the graphs above, show that this protein is relatively conformationally stable.

4.2   Example 2: An intrinsically disordered protein (2fft)

As compared to the conformationally stable protein above, an intrinsically disordered protein 2fft is much more flexible

Panel (b) shows that the states accessed per model are diverse and dramatically fluctuate over the entire range of R (this is especially true when compared to a stable protein, see above).

The diverse states occupied by each residue (Panels (c) and (d)) confirm the conformaational variation displayed by most residues (Panels (e) and (f) similarly show how most of the residues fluctuate dramatically).

Yet, interestingly, Panels (c) through (f) also show an unsusually stable region – residues 15 through 25 – which consistently display the same conformational (alpha-helical) state at R ~ 0.33 (interpreted as the color red in Panel (c)). This trend would be hard to recognize by simply looking at the structure (Panel (a)).

5   Publications

The Ramachandran number concept is discussed in the following manuscripts (this tool is discussed in the first reference):

1. Mannige (2018) “The Backmap Python Module: How a Simpler Ramachandran Number Can Simplify the Life of a Protein Simulator” Manuscript Prepared. Preprint available the manuscript/manuscript subdirectory of this repo.

2. Mannige, Kundu, Whitelam (2016) “The Ramachandran Number: An Order Parameter for Protein Geometry” PLoS ONE 11(8): e0160023. Full Text: https://doi.org/10.1371/journal.pone.0160023