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

v4.1.0 2023.3

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.

Installation:
```
  pip install "biobb_flexdyn>=4.1.0"
```
Usage: Python API documentation

Using ANACONDA:

Installation:

  conda install -c bioconda "biobb_flexdyn>=4.1.0"

Usage: With conda installation BioBBs can be used with the Python API documentation and the Command Line documentation

Using DOCKER:

Installation:

  docker pull quay.io/biocontainers/biobb_flexdyn:4.1.0--pyhdfd78af_0

Usage:

  docker run quay.io/biocontainers/biobb_flexdyn:4.1.0--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:4.1.0--pyhdfd78af_0

Usage:

  singularity exec biobb_flexdyn.sif <command>

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

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

(c) 2015-2024 Barcelona Supercomputing Center
(c) 2015-2024 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.