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 wrote a list of free books on the post Free Data Science Books. This book “Python for the Life Sciences …
NOTE: this post becoming too long, its content is now moved and updated on the page: PyMOL Resources PyMOL resources Summary This post provides resources on PyMOL What is PyMOL and how to get it The University of Wisconsin participates in the licensing of PyMOL Campus wide. License and software are available on the Campus …
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. (See more on the Wikipedia article Cryogenic electron microscopy.) The following links are videos meant to present cryo-EM visually. Unfortunately, …
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 sequence from one-letter to three-letter or vice versa? Easiest is on a listed web site. 3. How to write the …
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.
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).
Predicting protein three-dimensional (3D) structures given a linear sequence of amino acids. The AlphaFold2 breakthrough.
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 that it would be a “simple” 3D homology modeling problem, solved by common methods. It turns out that the protein …
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/ Using the javacript-based JMol web plug-in they provide easy to use, script-based interactive lessons detailing many structural aspect of biomolecules. …
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.