Summary This post is a summary of installation of AlphaFold2 onto a Macintosh with an M1 style (arm64) computer chip (i.e. not an Intel/AMD Chip.) This post started with the blog post Installing Alphafold2 on …
Molecular Graphics
3D Molecular Structures Analysis with NCBI iCn3D
NCBI tutorial: iCn3D hands-on workshop “I see in 3D” (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode […] – (Longer description.) …
PyMOL Stereo viewing
PyMOL Stereo viewing PyMOL can display stereo in many ways. Unless special equipment is available, the method is to split the PyMOL 3D view area in two with the command stereo on (and stereo …
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. …
Where is VirusWorld?
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 …
AlphaFold – How to interpret structures
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. …
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.
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/ …