Virusworld. was hosted since its inception at the Institute for Molecular Virology in 1993/1994 at the dawn of the World Wide Web and was retired on the first week of July 2022. I was the main author and curator of the web site which was started to disseminate virus depictions based on X-ray crystallography …
w3schools: Learn to Code On the w3schools site I was surprised to find a lot more than informational tutorial for Web coding such as CSS or PHP. The site offers a large number of well organized, self-paced tutorials on a much larger scale. Coding languages Here are a few that I find particularly useful to …
Learn X in Y minutes In the past we had “flash cards” to memorize and review materials. This site Learn X in Y minutes has one-page reminders that can be used to re-learn material or get some idea of what the subject is about. For example I wrote a series of 4 posts titled Do …
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 …
Google Docs is Free Google Docs is a free, web-based document creator system to create and collaborate on online documents in real-time and from any device. The type of documents that can be created can be text, notes, spreadsheet, drawing, slides, and web pages, each with a separate editor. The Wikipedia entry for Google Docs …
High Throughput Computing (HTC) First a note: HTC is meant for a large number of small to medium size jobs. HTC is different than HPC (High Performance Computing) that would run large size jobs that require a high memory (RAM) footprint, and/or extremely large data files. Biochemistry Department personnel can obtain access to the in-door …
Sometimes a very simple command can accomplish amazing tasks. Recently I had a list with alternating entries on every other line with about 200 lines, and lots of uneven text. But I wanted to have 2 columns instead. A quick online search let me find a new way of using a familiar command called …
3D Protein structure prediction (4) This YouTube video from the European Bioinformatics Institute – EMBL-EBI webinar was recorded on 08 September 2021 This webinar will introduce AlphaFold system for prediction and interpretation of protein structures. This webinar is designed for experimental biologists who wish to understand the strengths and limitations of AlphaFold and use 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).