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biobb_wf_godmd

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).

https://github.com/bioexcel/biobb_wf_godmd

Science Score: 57.0%

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    Low similarity (4.0%) to scientific vocabulary
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Repository

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).

Basic Info
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  • Stars: 0
  • Watchers: 5
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed 12 months ago
Metadata Files
Readme License Citation

README.md

Protein conformational transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).

Examples shown are the calculation of the conformational transition for the Adenylate Kinase protein, from the closed state (PDB Code 1AKE) to the open state (PDB Code 4AKE). Adenylate Kinases are phosphotransferase enzymes that catalyze the interconversion of the various adenosine phosphates (ATP, ADP, and AMP), and are known to undergo large conformational changes during their catalytic cycle.

The code wrapped is the GOdMD method, developed in the Molecular Modeling and Bioinformatics group (IRB Barcelona). GOdMD determines pathways for conformational transitions in macromolecules using discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques. A web implementation of the method can be found here: https://mmb.irbbarcelona.org/GOdMD/index.php

Exploration of conformational transition pathways from coarse-grained simulations.
Sfriso P, Hospital A, Emperador A, Orozco M.
Bioinformatics, 129(16):1980-6.
Available at: https://doi.org/10.1093/bioinformatics/btt324

Settings

Biobb modules used

  • biobb_godmd: Tools to compute protein conformational transitions using GOdMD.
  • biobb_io: Tools to fetch biomolecular data from public databases.
  • biobbstructureutils: Tools to modify or extract information from a PDB structure.
  • biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

Auxiliary libraries used

  • emboss: Software that automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.
  • jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
  • plotly: Python interactive graphing library integrated in Jupyter notebooks.
  • nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
  • simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.

Conda Installation and Launch

console git clone https://github.com/bioexcel/biobb_wf_godmd.git cd biobb_wf_godmd conda env create -f conda_env/environment.yml conda activate biobb_wf_godmd jupyter-notebook biobb_wf_godmd/notebooks/biobb_wf_godmd.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
biobb_wf_godmd/docs/requirements.txt pypi
  • recommonmark *
  • sphinx_rtd_theme *
.github/workflows/citation.yaml actions
  • actions/checkout v2 composite
conda_env/environment.yml conda
  • biobb_analysis 4.2.0
  • biobb_godmd 4.2.0
  • biobb_io 4.2.0
  • biobb_structure_utils 4.2.0
  • emboss
  • jupyter
  • nglview
  • plotly
  • simpletraj
binder/environment.yml pypi