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. The only exception to this description is constituted by the installation of software for MD simulations and protein structure prediction, which have to be installed before starting the tutorials. Therefore, we created an additional tutorial for installation of this software.

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	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, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], NGL Viewer [6]
Lab.09.Docker	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, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], NGL Viewer [6]
Lab.10.Docker	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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