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biobb_wf_structure_checking

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation using the BioExcel Building Blocks library (biobb).

https://github.com/bioexcel/biobb_wf_structure_checking

Science Score: 44.0%

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Repository

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation using the BioExcel Building Blocks library (biobb).

Basic Info
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  • Stars: 0
  • Watchers: 5
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

Molecular Structure Checking using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

Structure checking is a key step before setting up a protein system for simulations. A number of common issues found in structures at Protein Data Bank may compromise the success of the simulation, or may suggest that longer equilibration procedures are necessary.

The workflow shows how to:

  • Run basic manipulations on structures (selection of models, chains, alternative locations
  • Detect and fix amide assignments and wrong chiralities
  • Detect and fix protein backbone issues (missing fragments, and atoms, capping)
  • Detect and fix missing side-chain atoms
  • Add hydrogen atoms according to several criteria
  • Detect and classify atomic clashes
  • Detect possible disulfide bonds (SS)

An implementation of this workflow in a web-based Graphical User Interface (GUI) can be found in the https://mmb.irbbarcelona.org/biobb-wfs/ server (see https://mmb.irbbarcelona.org/biobb-wfs/help/create/structure#check).

Settings

Biobb modules used

  • biobb_io: Tools to fetch biomolecular data from public databases.
  • biobbstructureutils: Tools to modify or extract information from a PDB structure.
  • biobb_model: Tools to check and model 3D structures, create mutations or reconstruct missing atoms.
  • biobb_amber: Tools to setup and simulate atomistic MD simulations using AMBER MD package.
  • biobb_chemistry: Tools to perform chemoinformatics on molecular structures.

Auxiliary libraries used

  • modeller: Software used for homology or comparative modeling of protein three-dimensional structures.
  • jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
  • nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.

Conda Installation and Launch

console git clone https://github.com/bioexcel/biobb_wf_structure_checking.git cd biobb_wf_structure_checking conda env create -f conda_env/environment.yml conda activate biobb_wf_structure_checking jupyter-notebook biobb_wf_structure_checking/notebooks/biobb_wf_structure_checking.ipynb

Tutorial

Click here to view tutorial in Read the Docs

Click here to execute tutorial in Binder

Click here to open tutorial in Google Colab

Version

2025.1 Release

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 Horizon Europe 101093290, EU H2020 823830, EU H2020 675728).

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

Owner

  • Name: BioExcel
  • Login: bioexcel
  • Kind: organization

Center of Excellence for Computational Biomolecular Research

Citation (CITATION.cff) 

abstract: "BioExcel Building Blocks (BioBB) library. BioBB's are built as Python wrappers to provide an interoperable architecture. BioBB's have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments."
authors:
  - affiliation: "Barcelona Supercomputing Center (BSC)"
    family-names: "Andrio"
    given-names: "Pau"
    orcid: "https://orcid.org/0000-0003-2116-3880"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Hospital"
    given-names: "Adam"
    orcid: "https://orcid.org/0000-0002-8291-8071"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Bayarri"
    given-names: "Genís"
    orcid: "https://orcid.org/0000-0003-0513-0288"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "García"
    given-names: "Agustín"
    orcid: "https://orcid.org/0009-0002-2159-965X"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Chaves"
    given-names: "Rubén"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University of Barcelona (UB)"
    family-names: "Orozco"
    given-names: "Modesto"
    orcid: "https://orcid.org/0000-0002-8608-3278"
  - affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
    family-names: "Gelpí"
    given-names: "Josep Ll."
    orcid: "https://orcid.org/0000-0002-0566-7723"
    email: "gelpi@ub.edu"
cff-version: 1.2.0
date-released: "2019-09-10"
keywords:
  - "BioExcel"
  - "BioBB"
  - "Bioinformatics"
  - "Computational Biology"
  - "Biomolecular Workflows"
license: "Apache-2.0"
message: "If you use this dataset, please cite it using the metadata from this file."
repository-code: "https://github.com/bioexcel/biobb"
title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
doi: "10.1038/s41597-019-0177-4"
url: "https://mmb.irbbarcelona.org/biobb/"
version: 5.0.0
preferred-citation:
  type: "article"
  authors:
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Andrio"
      given-names: "Pau"
      orcid: "https://orcid.org/0000-0003-2116-3880"
    - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
      family-names: "Hospital"
      given-names: "Adam"
      orcid: "https://orcid.org/0000-0002-8291-8071"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Conejero"
      given-names: "Javier"
      orcid: "https://orcid.org/0000-0001-6401-6229"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Jordà"
      given-names: "Luis"
      orcid: "https://orcid.org/0000-0002-9407-9703"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Del Pino"
      given-names: "Marc"
      orcid: "https://orcid.org/0000-0001-5565-7577"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Laia"
      given-names: "Codó"
      orcid: "https://orcid.org/0000-0002-6797-8746"
    - affiliation: "University of Manchester (UOM)"
      family-names: "Soiland-Reyes"
      given-names: "Stian"
      orcid: "https://orcid.org/0000-0001-9842-9718"
    - affiliation: "University of Manchester (UOM)"
      family-names: "Goble"
      given-names: "Carole"
      orcid: "https://orcid.org/0000-0003-1219-2137"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Lezzi"
      given-names: "Daniele"
      orcid: "https://orcid.org/0000-0001-5081-7244"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Badia"
      given-names: "Rosa M"
      orcid: "https://orcid.org/0000-0003-2941-5499"
    - affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University  of Barcelona (UB)"
      family-names: "Orozco"
      given-names: "Modesto"
      orcid: "https://orcid.org/0000-0002-8608-3278"
    - affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
      family-names: "Gelpí"
      given-names: "Josep Ll."
      orcid: "https://orcid.org/0000-0002-0566-7723"
      email: "gelpi@ub.edu"
  doi: "10.1038/s41597-019-0177-4"
  journal: "Nature Scientific Data"
  month: 9
  start: 169
  title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
  issue: 1
  volume: 6
  year: 2019

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Dependencies

.github/workflows/inactive_issues.yml actions
  • actions/stale v5 composite
binder/environment.yml pypi
conda_env/environment.yml pypi