biobb-structure-checking

biobb_structure_checking

Introduction

Biobb_structure_checking provides a series of functions to check the quality of a 3D structure intended to facilitate the setup of a molecular dynamics simulation of protein or nucleic acids systems.

Biobb_structure_checking package allows to configure the system (selection of model/chains,alternative location, addition of disulfide bonds and hydrogen atoms, side chain mutations), to detect and fix structure errors (missing side chain atoms, backbone breaks, amide assignments, incorrect chirality). It works with structures obtained from the Protein Data Bank or user provided.

The Biobb_structure_checking package provides a command line utility (check_structure) and a python API.

The latest documentation of this package can be found in our readthedocs site: latest package documentation.

Version

v3.15.6 March 2025

Requirements

• Biopython

Optional requirements

• psutil (required for --debug, included in conda pkg.)
• Modeller (required for some functionalities, not included in conda pkg.)
• jupyter & nglview (required for demonstration notebooks, not included in conda pkg.)

Installation

Using PIP:

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

• Installation:

    pip install "biobb_structure_checking>=3.15.0"
  

• Usage: Python API documentation.

Using ANACONDA:

• Installation:

    conda install -c bioconda "biobb_structure_checking>=3.15.0"
  

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

Copyright & Licensing

This software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the BSC (https://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (https://bioexcel.eu/). BioExcel is funded by the European Union Horizon 2020 program under grant agreements 823830, 675728 and by the EuroHPC Joint Undertaking and Sweden, Netherlands, Germany, Spain, Finland and Norway under grant agreement 101093290 funded by the European Commission.

• (c) 2015-2025 Barcelona Supercomputing Center
• (c) 2015-2025 Institute for Research in Biomedicine

Licensed under the GNU Lesser General Public License v2.1.