Summary “Explore how David Baker, Demis Hassabis, and John Jumper won the 2024 Nobel Prize in Chemistry for their advances in computer-assisted protein design.” Video: How AI Cracked the Protein Folding Code and Won a Nobel Prize This 22min19 video provides a very good explanation of the origins of the research in protein structure, from …
Summary The NIH offers 2D bioart (bioart.niaid.nih.gov) with a public domain license, and collections of 3D models (3d.nih.gov) Free 2D Bio Art The National Institute of Allergy and Infectious Diseases (NIAID), one of the 27 Institutes and Centers of the National Institutes of Health (NIH), has released a series of sketch art that may prove …
Summary Run the ColabFold version of AlphaFold2 on your laptop (slow without GPU) or on a large Linux cluster. The full tutorial with scripts is located at ColabFold with HTCondor What is AlphaFold2 Excerpt from a previous post (Five ways to run AlphaFold) AlphaFold can accurately predict 3D models of protein structures by providing an …
Summary Workshop Series available on Campus on R and Python. (For more details see further below.) – Biochem – Social Science Computing Cooperative (SSCC) – UW Libraries – SSteenbock Library Workshops – Computational Biology, Ecology, & Evolution (ComBEE) Study Groups R and Python at Biochem R and Python “Clubs” were established in late 2022. The …
Summary We run a script to compute the distance between 2 atoms in a series of PDB files with identical molecules in different conformations and save the distance results into a plain text file. No GUI PyMOL In previous posts I explained how we can use PyMOL as a command-line tool from a Terminal when …
Summary The new Numpy 2.0 is not compatible with many other packages, as I discovered after many lost hours. The final Docker images can be downloaded from alleleanalyzer. NumPy in a Docker I was interested to implement a process involving Python packages from a paper published in 2019: “AlleleAnalyzer: a tool for personalized and allele-specific …
R and Tidyverse Tabular Data Analysis I have updated the Tabular data analysis with R and Tidyverse course that analyze environmental health data from National Health and Nutrition Examination Survey (NHANES) a survey research program conducted by the National Center for Health Statistics (NCHS) to assess the health and nutritional status of adults and children …
“Data visualisation principles for enhancing effective scientific communication” Webinar Announcement: “Live Training” This webinar will provide an introduction to data visualisation principles. It includes a review of basic concepts and showcases tools to improve your understanding and use of data visualisation for improved accessibility to your research. Link: https://www.ebi.ac.uk/training/events/data-visualisation-principles-enhancing-effective-scientific-communication/ Quick Info: Register Date: 26 June …
Summary Compute biological assembly from coordinates with a python script. Symmetry X-ray crystallography solved the mathematical problem to provide 3D (cartesian) coordinates but the resulting “asymmetric unit cell” does not necessarily represent the biological structure. The Protein Data Bank (PDB) now provides options to download the biological entity, which can contain a lesser number than …
Computational Modeling This is the general title of a new Tutorials pull-down menu that will be populated with new or updated tutorials. It can be found within the Tutorials menu list as Computational Modeling The very first tutorial is the result of an update to a Rosetta tutorial for “ligand docking” and adapt the Linux-based …