https://github.com/giorginolab/ibm3202

Google Colab Tutorials for IBM3202

https://github.com/giorginolab/ibm3202

Repository

Google Colab Tutorials for IBM3202

https://github.com/giorginolab/ibm3202/blob/master/

# Cloud-based Tutorials on Structural Bioinformatics
### Institute for Biological and Medical Engineering [(IIBM)](http://iibm.uc.cl), Pontificia Universidad Catolica de Chile
### ANID  Millennium Science Initiative Program  Millennium Institute for Integrative Biology [(iBio)](http://ibio.cl)
##
## 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 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab00_software.ipynb) | Installing Software on Google Colab for IBM3202 tutorials                           | pyRosetta [1], GROMACS [2], SBM-enhanced GROMACS [3]                                                        |
| Lab.01 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab01_intro.ipynb) | Warm-up on Colab and Brief Review of Biomolecular Databases                         |                                                                                                             |
| Lab.02 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab02_molviz.ipynb) | Visualizing and Comparing Molecular Structures in Google Colab using py3Dmol        | Biopython [4], py3Dmol [5], NGL Viewer [6]                                                                  |
| Lab.03 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab03_phylo.ipynb) | Phylogenetic Analysis using biopython and RAxML                                     | Biopython [4], miniconda [7], MAFFT [8], ModelTest-ng [9], RAxML-ng [10]                                    |
| Lab.04 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab04_cm.ipynb) | Comparative Modeling using MODELLER                                                 | Biopython [4], py3Dmol [5], MODELLER [11]                                                                   |
| Lab.05 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab05_MP_rosetta.ipynb) | Membrane Protein Modelling using PyRosetta                                          | pyRosetta [1], py3Dmol [5]                                                                                  |
| Lab.06 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab06_docking.ipynb) | Molecular Docking on Autodock                                                       | Biopython [4], py3Dmol [5], miniconda [7], Open Babel [12], pdb2pqr [13], MGLTools [14], Autodock Vina [15] |
| Lab.07 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab07_MDsims.ipynb) | Molecular Dynamics on GROMACS                                                       | GROMACS [2], Biopython [4], py3Dmol [5], NGL Viewer [6]                                                     |
| Lab.08 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab08_MDanalysis.ipynb) | Trajectory Analysis using MDanalysis                                                | py3Dmol [5], MDAnalysis [16]                                                                                |
| Lab.09 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab09_SMOGfolding.ipynb) | Folding Simulations using Structure-Based Models                                    | SMOG2, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], NGL Viewer [6]                                 |
| Lab.10 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab10_SMOGdual.ipynb) | Conformational changes using Structure-Based Models                                 | SMOG2, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], NGL Viewer [6]                                 |
| Lab.11 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab11_rnaDCA.ipynb) | Prediction of interactions from the coevolutionary analysis of sequence information | Biopython [4], py3Dmol [5], infernal [17], pyDCA [18]                                                       |
| Lab.12 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/lab12_abinitioRosetta.ipynb) | Protein folding ab initio using Rosetta                                             | pyRosetta [1], Biopython [4], py3Dmol [5]                                                                   |

## Tutorials  2021

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

| Tutorial | Description                           | Software                                                        |
|--------|-------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------|
| Lab.13 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pb3lab/ibm3202/blob/master/tutorials/2021/lab13_protDCASBM.ipynb) | Combining DCA and SBM to predict protein structures | SMOG2, SBM-enhanced GROMACS [3], Biopython [4], py3Dmol [5], pyDCA [18]                                       |

## Authors
Felipe Engelberger, Pablo Galaz-Davison, Graciela Bravo, Maira Rivera and Csar A. Ramrez Sarmiento.

**Protein Biophysics, Biochemistry and Bioinformatics Lab [(PB3)](https://pb3.sitios.ing.uc.cl)**, 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, Ramrez-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](https://dx.doi.org/10.1021/acs.jchemed.1c00022)

## Contributions and Code of Conduct

Please **read** our rules on [Contributions and Code of Conduct](https://github.com/pb3lab/ibm3202/blob/master/contributions.md) before making any changes.

## References
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