Jupyter Notebook Molecular Structure Checking Version 1
View on GitHub
Download RO-CrateMolecular 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).
- (c) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 Institute for Research in Biomedicine
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-1fcfe017
Creators and Submitter
Views: 884 Downloads: 494
Created: 5th Mar 2024 at 08:36
Last updated: 5th Mar 2024 at 08:36
TagsThis item has not yet been tagged.
AttributionsNone
Collections
Interactive Jupyter...
Related items
https://orcid.org/0000-0003-0513-0288
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...
