BioExcel Building Blocks tutorials: Protein Conformational Transitions

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 (biobb).

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Topics

Biomolecular simulation Data visualisation Molecular modelling Protein sites, features and motifs Protein structure analysis Protein structure analysis

Collections

BioExcel

Details

License:: Apache-2.0
Maturity:: Emerging
Cost:: Free of charge
Tool Type:: workflow
Operating Systems:: Linux, Mac, Windows
Programming Languages:: Python
Added:: 8/31/2023
Last Updated:: 6/23/2026

Operations

Data Inputs & Outputs

Molecular dynamics

Inputs

Protein structure
- PDB

Outputs

Trajectory data
- PCAzip
- mdcrd

Publications

DOI: 10.1038/s41597-019-0177-4

PMID: 31506435

PMCID: PMC6736963

DOI: 10.1093/bioinformatics/btt324

PMID: 23740746

Documentation

Other

https://biobb-wf-godmd.readthedocs.io/en/latest/index.html

Documentation in Read the Docs

Downloads

Source code
Version: 1.0
https://github.com/bioexcel/biobb_wf_godmd
Source Code in GitHub

Links

Repository

https://github.com/bioexcel/biobb_wf_godmd

(Source Code in GitHub)

Other

https://biobb-wf-godmd.readthedocs.io/en/latest/index.html

(Tutorial in Read the Docs)

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