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 …
Summary (Free) Steenbock Library: R and python series (Free) SSCC (Social Science Computing Cooperative): SSCC Training Classes (low cost for UW) Software Carpentry: Software Carpentry @ UW–Madison Low cost registration ends January 5, 2022 See also the general Calendar listing . Library workshops Note: these workshops fill-in fast… Individual workshop descriptions and instructors list. Registration required. …
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. …
Summary Check the Calendar listing for data analysis workshops links and registration forms. Steenbock and SSCC workshops Library workshops Note: these workshops fill-in fast… Individual workshop descriptions and instructors list. Please email Heather Shimon, heather.shimon@wisc.edu with questions or to be added to our email list for updates. Registration required. Registration is by workshop, not for the …
Building a Protein Backbone from alpha-Carbon Files containing only C-alpha ATOM records can be the result of modeling but can also be a step in structure resolution. Theoretical models are now deposited in the ModelArchive(*). How can we obtain a complete structure for further investigation, e.g. to use in a molecular graphics software? Using Sybyl? In …
Summary There is a vast archive of free content on the Internet Archive and web pages and documents preserved since about 1996 on the Wayback Machine that allows finding and retrieving web pages and documents that have vanished from the every day web and are not indexed in the search engines. An example is provided. Vanishing content …
I have been a Macintosh user since 1986 but it is still necessary once in a while to access a Windows system and that is why VMWare Fusion is installed on my iMac which has a separate partition on its drive called BootCamp that contains the Windows system. There are different ways to set-up using …
The message The essential message is this: stop using Copy/Paste from one program to another (e.g. a chart from Excel to Word) as this is a manual process that is not reproducible and can easily get out of sync if new data need to be incorporated and the report reconstructed anew. The solution is to …