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biobb_flexdyn

Introduction

biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins. biobb_flexdyn allows the generation of protein conformational ensembles from 3D structures and the analysis of its molecular flexibility. It is based on the work done in the flexdyn implementation study from the 3D-Bioinfo ELIXIR structural community (https://elixir-europe.org/communities/3d-bioinfo). Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v5.0.0 2024.2

Installation

Using PIP:

Important: PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA or DOCKER.

Using ANACONDA:

Using DOCKER:

  • Installation:

      docker pull quay.io/biocontainers/biobb_flexdyn:5.0.0--pyhdfd78af_0
    
  • Usage:

      docker run quay.io/biocontainers/biobb_flexdyn:5.0.0--pyhdfd78af_0
    

Using SINGULARITY:

MacOS users: it’s strongly recommended to avoid Singularity and use Docker as containerization system.

  • Installation:

      singularity pull --name biobb_flexdyn.sif https://depot.galaxyproject.org/singularity/biobb_flexdyn:5.0.0--pyhdfd78af_0
    
  • Usage:

      singularity exec biobb_flexdyn.sif <command>
    

The command list and specification can be found at the Command Line documentation.