PBTools

Protein Block Molecular Dynamics Tools

PBTools is a program to perform analysis on molecular dynamics protein sequences encoded as Protein Blocks. Protein Blocks are structures defined by De Brevern et al. to analyze local conformations of proteins.
The program a simple Python re-implementation of GSATools by Pandini et al. using these Protein Blocks as a structural alphabet.

The documentation can be found here.
Try the demo with Binder:

Requirements

• Python >= 3.6
• PBXplore
• pandas
• numpy
• NetworkX

Installation

From GitHub

Install directly the git development version with:

pip install git+https://github.com/lilianyc/pbtools.git

Developer mode

Install conda

Clone the repository:

$ git clone https://github.com/lilianyc/pbtools
$ cd pbtools

Create conda environment:

$ conda env create -f environment.yml

Remark: for a fully reproducible environment, you could also use:

$ conda env create -f environment.lock.yml

Conda might give some errors with packaging

Activate conda environment:

$ conda activate PBTools

Install local package:

$ pip install -e .

Quickstart

The script can take either PDB files or a trajectory and topology file.

It will return a csv of an upper triangular Mutual Information matrix for each position of the Protein Block sequence.

Options

• -h, --help:
  Provide a help page

• -v, --version:
  Provide the version

• -o, --output:
  Give the name of the output file

• -n, --network:
  Give the name of the network file

• -p, --pdb:
  Name of PDB file(s) or a directory containing PDB files

• -x:
  Name of the trajectory file

• -g:
  Name of the topology file

Examples

After installing PBTools, you can use the Command-Line Interface.

Using

$ pbtools -o matrix.csv -p 1BTA.PDB

will create matrix.csv, a file containing the Mutual Information matrix.

Credits

• Binder

  • Jupyter et al., "Binder 2.0 - Reproducible, Interactive, Sharable Environments for Science at Scale." Proceedings of the 17th Python in Science Conference. 2018. 10.25080/Majora-4af1f417-011

• GSATools

  • Pandini A, Fornili A, Fraternali F, Kleinjung J. GSATools: analysis of allosteric communication and functional local motions using a structural alphabet. Bioinformatics 29(16):2053–2055. https://doi.org/10.1093/bioinformatics/btt326 (2013)

• PBXplore

  • Barnoud J, Santuz H, Craveur P, Joseph AP, Jallu V, de Brevern AG, Poulain P, PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks. PeerJ 5:e4013 https://doi.org/10.7717/peerj.4013 (2017).

• Protein Blocks

  • A. G. de Brevern, C. Etchebest, S. Hazout, Bayesian Probabilistic Approach for Predicting Backbone Structures in Terms of Protein Blocks. Proteins 41:271-87 http://dx.doi.org/10.1002/1097-0134(20001115)41:3%3C271::AID-PROT10%3E3.0.CO;2-Z (2000).