Cloud-based Tutorials on Structural Bioinformatics

Institute for Biological and Medical Engineering (IIBM), Pontificia Universidad Catolica de Chile

ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio)

Introduction

This is a set of twelve (12) tutorials on protein folding, function, structure, dynamics and evolution for distance learning using the Google Colab free cloud-computing environment.

These tutorials were created between Jun-Sep 2018 as part of the IBM3202 Molecular Modelling and Simulation module for execution of standalone computers and then fully redesigned between Jun-Jul 2020 for full execution over Google Colab and remote accesibility via web browsers due to the COVID-19 pandemic.

Each tutorial includes a brief introduction of the activities to be performed, installation instructions of the open-source software to be used in each session and several programming, visualization and data analysis activities to be achieved during the tutorial.

Description of the Tutorials

The following is a brief description of each tutorial, along with the open-source software used for each task:

Tutorial	Description	Software
Lab.00	Installing Software on Google Colab for IBM3202 tutorials (OBSOLETE)	pyRosetta [1], GROMACS [2], SBM-enhanced GROMACS [3]
Lab.01	Warm-up on Colab and Brief Review of Biomolecular Databases
Lab.02	Visualizing and Comparing Molecular Structures in Google Colab using py3Dmol	Biopython [4], py3Dmol [5], NGL Viewer [6]
Lab.03	Phylogenetic Analysis using biopython and RAxML	Biopython [4], miniconda [7], MAFFT [8], ModelTest-ng [9], RAxML-ng [10]
Lab.04	Comparative Modeling using MODELLER	Biopython [4], py3Dmol [5], MODELLER [11]
Lab.05	Membrane Protein Modelling using PyRosetta	pyRosetta [1], py3Dmol [5]
Lab.06	Molecular Docking on Autodock	Biopython [4], py3Dmol [5], miniconda [7], Open Babel [12], pdb2pqr [13], MGLTools [14], Autodock Vina [15]
Lab.07	Molecular Dynamics on GROMACS	GROMACS [2], Biopython [4], py3Dmol [5], NGL Viewer [6]
Lab.08	Trajectory Analysis using MDanalysis	py3Dmol [5], MDAnalysis [16]
Lab.09	Folding Simulations using Structure-Based Models	SMOG2 Docker, udocker, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], NGL Viewer [6]
Lab.10	Conformational changes using Structure-Based Models	SMOG2 Docker, udocker, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], NGL Viewer [6]
Lab.11	Prediction of interactions from the coevolutionary analysis of sequence information	Biopython [4], py3Dmol [5], infernal [17], pyDCA [18]
Lab.12	Protein folding ab initio using Rosetta	pyRosetta [1], Biopython [4], py3Dmol [5]

Tutorials – 2021 & 2023

The following is a brief description of each tutorial generated in 2021 & 2023, along with the open-source software used for each task:

Tutorial	Description	Software
Lab.13	Combining DCA and SBM to predict protein structures	SMOG2, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], pyDCA [18]
Lab.14	Combining MSA Transformer and SBM to predict protein structures	SMOG2, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], MSA Transformer

Tutorial for Structural Biology in 2022

Tutorial	Description	Software
Lab.15	Combining ColabFold and GROMACS to predict and simulate protein structures	GROMACS [2], Biopython [4], py3Dmol [5], NGL Viewer [6], ColabFold [19]

Authors

Felipe Engelberger, Pablo Galaz-Davison, Graciela Bravo, Maira Rivera and César A. Ramírez Sarmiento.

Protein Biophysics, Biochemistry and Bioinformatics Lab (PB³), Institute for Biological and Medical Engineering (IIBM) / Millenium Institute for Integrative Biology (iBio)

Cite us!

If you use these tutorials in your research/teaching, please cite us!:

Engelberger F, Galaz-Davison P, Bravo G, Rivera M, Ramírez-Sarmiento CA (2021) Developing and Implementing Cloud-Based Tutorials that Combine Bioinformatics Software, Interactive Coding and Visualization Exercises for Distance Learning on Structural Bioinformatics. J Chem Educ 98(5): 1801-1807. doi: 10.1021/acs.jchemed.1c00022

Contributions and Code of Conduct

Please read our rules on Contributions and Code of Conduct before making any changes.

References

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