Jupyter Notebook Molecular Structure Checking
Version 1

Workflow Type: Jupyter

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).

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).

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

Version History

Version 1 (earliest) Created 5th Mar 2024 at 08:36 by Genís Bayarri

Initial commit

Frozen Version-1 fcfe017
help Creators and Submitter
Hospital, A., & Bayarri, G. (2024). Jupyter Notebook Molecular Structure Checking. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.775.1

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Created: 5th Mar 2024 at 08:36

Last updated: 5th Mar 2024 at 08:36

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