Summary Molecule of the Month In the year 2000 David Goodsell started to provide stories on the The Protein Data Bank web site as the “molecule of the month” with his unique style that was later made available by the Qutemol software, unfortunately not updated since 2007 and therefore no longer working on many systems, …
Summary The National Center for Biotechnology Information (NCBI) offers events, including workshops hands-on, interactive training sessions. All events are listed on the NCBI Outreach Events page. Workshop recordings and materials remain available after the live sessions. NCBI Outreach Events The National Center for Biotechnology Information (NCBI) is a division of the National Library of Medicine …
Summary PyMOL command scripts are available natively and within Docker images. PyMOL Scripts PyMOL offers a very easy-to-use graphical user interface (GUI) to manipulate loaded molecule, and alter the appearance and coloring options. However, while this is easy, it is not the “best way” to use PyMOL if one wants to be able to reproduce …
Summary This article describes running AlphaFold2 with full databases at the UW–Madison Center for High Throughput Computing (CHTC) and is part of an article series titled Five ways to run AlphaFold. CHTC cluster, HTCondor, Containerization The UW–Madison Center for High Throughput Computing (CHTC) offers free computing accounts for all UW–Madison personnel and offer the full …
Summary Computing a PNG image for each of 1,000 PDB files as a cartoon, color-coded by B factor. PyMOL without GUI PyMOL is routinely used by Biologists to illustrate molecules, using the graphical user interface (GUI.) However, there are situations where it may be beneficial to run PyMOL without using the mouse. I recently computed …
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 …
What is Augmented Reality? Augmented Reality (AR) is an exciting technology that overlays virtual elements on top of the real world, allowing for a unique and immersive user experience. The Apple AR platform only uses the web browser “Safari” and does not require any plug-in or specialized software, only that portable electronics (iPhone, iPad) have …
Intelligent Systems for Molecular Biology – in Madison The International Society for Computational Biology (ISMB) Conference held the Intelligent Systems for Molecular Biology (ISMB) in Madison in July 2022. Conference details are still available online, but more importantly a special “Bioinformatics” journal issue has been compiled from the proceedings of this conference: Most articles link to …
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.) This workshop is designed for life scientists with some (intermediate) expertise in structural biology. The topics of structure prediction, molecular …