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biobb_wf_haddock

This tutorials aim to illustrate the process of protein-protein docking, step by step, using HADDOCK with the BioExcel Building Blocks library (biobb).

https://github.com/bioexcel/biobb_wf_haddock

Science Score: 44.0%

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    Low similarity (3.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

This tutorials aim to illustrate the process of protein-protein docking, step by step, using HADDOCK with the BioExcel Building Blocks library (biobb).

Basic Info
  • Host: GitHub
  • Owner: bioexcel
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 1.16 MB
Statistics
  • Stars: 3
  • Watchers: 8
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created 9 months ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

Protein-protein Docking tutorial using HADDOCK with the BioExcel Building Blocks (biobb)

Based on the official HADDOCK3 Antibody-antigen modelling tutorial.

This tutorial aims to illustrate the process of protein-protein docking, step by step, using HADDOCK3 with the BioExcel Building Blocks library (biobb). The particular systems used in this tutorial are the Interleukin-1β (IL-1β) antigen (PDB code 4I1B) and the gevokizumab antibody (PDB code 4G6K). The complex is also available under the PDB code 4G6M.

Settings

Biobb modules used

  • biobb_io: Tools to fetch biomolecular data from public databases.
  • biobbpdbtools: Swiss army knife for manipulating and editing PDB files.
  • biobb_haddock: Module collection to compute information-driven flexible protein-protein docking.

Auxiliary libraries used

  • 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_haddock.git cd biobb_wf_haddock conda env create -f conda_env/environment.yml conda activate biobb_wf_haddock jupyter-notebook biobb_wf_haddock/notebooks/biobb_wf_haddock_aa.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

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

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 7
  • Fork event: 1
  • Create event: 2
Last Year
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 7
  • Fork event: 1
  • Create event: 2

Dependencies

.github/workflows/citation.yaml actions
  • actions/checkout v3 composite
  • peter-murray/workflow-application-token-action v3 composite
.github/workflows/inactive_issues.yml actions
  • actions/stale v5 composite
binder/environment.yml pypi
biobb_wf_haddock/docs/requirements.txt pypi
  • recommonmark *
  • sphinx_rtd_theme *
conda_env/environment.yml pypi