Summary Pose is a Python library for building and manipulating protein molecular structures. Builds with L- and D- amino acids or a mixture; can open existing PDB structures. Computes many molecular properties. Pose Library Pose is a Python library for building and manipulating protein molecular structures. From an amino acid sequence the user can create …
What is AlphaFold How to access AlphaFold There are multiple options to access AlphaFold. Here are four options using the limited databases. One options for the full databases. Using limited Databases: 1.) Casual users can use “Google Colab” with a web browser. Familiarity with Jupyter Notebook for running Python is helpful. The service is free …
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 Apple Silicon. The installation will require about 8Gb of space. Installing AlphaFold2 AlphaFold2 is a trained Machine Learning set of …
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: The Biochem 660 PyMOL tutorial book has been split in 4 PDFs for easier read and download: Preamble For many years I participated in the teaching of Prof. Ann Palmenberg classes, in particular teaching about molecular graphics on the Desktop at a time when computer use in the classroom was not yet preeminent. This …