Summary This book will be used to learn Python in workshop settings. For Biologists, Life Scientists There are many books, even free books, with the objective to teach Python or other programming languages. I previously …
biochemistry
PyMOL resources, books and references
NOTE: this post becoming too long, its content is now moved and updated on the page: PyMOL Resoruces PyMOL resources Summary This post provides resources on PyMOL What is PyMOL and how to get it …
Visual introduction to CryoEM
Cryo-Electron Microscopy Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures (i.e. very cold!.) For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. …
1to3 and 3to1 peptide sequence conversion
Summary 1. How to easily convert a string of character to appear one character per line> Either of: echo “abcdefg” | fold -w1 echo “abcdefg” | grep -o . 2. How to convert amino acid …
AlphaFold – run from ChimeraX
The new ChimeraX menu “Tools > Structure Prediction > AlphaFold” provides a simple interface to run AlphaFold2 Colab that does not require the user to know how to use a Jupyter Notebook.
AlphaFold code
DeepMind and Google have created a method to access the code on GitHub. All the details to install AlphaFold locally are on the “readme” page, visible on the lower portion of the GitHub page ColabFold (See my Blog: Google colab is a free cloud notebook environment).
AlphaFold background
Predicting protein three-dimensional (3D) structures given a linear sequence of amino acids. The AlphaFold2 breakthrough.
Computing residues per turn in an alpha helix
Single mutation to be modeled I recently had an interesting challenge, that of creating a molecular model of a protein expressed from a gene with a newly identified single amino acid mutation. I (wrongly) assumed …
The Fundamentals of Biochemistry: Interactive Tutorials
The Fundamentals of Biochemistry: Interactive Tutorials from Colorado State University was created by Dr. David Fahrney and edited by Ben Robinson. The 10th edition contains 10 interactive tutorials of the planned 16 chapters. Link: https://bc401.bmb.colostate.edu/ …
Tabular data analysis with R and Tidyverse
Does data analysis feel like the impossible job of “catching the moon?”
Fortunately R and RStudio are great tools to analyze data and illustrate conclusions, while at the same time keeping records and create “live” documents that can be updated with “just one click.”
The material is written in a way that is conducive to “learn by doing” following demonstrations and examples. All code and all necessary materials and files are available and therefore it is possible to learn and acquire proficiency on one’s own with this course content.