Summary ChatMol is a ChatGPT plugin that offers a Free chatlite version that does not require an API key. ChatMol ChatMol is a PyMOL plugin based on large language models, that provide a conversational interface …
biochemistry
Nobel-Winning AlphaFold2 and RosettaFold: Cracking the Protein Folding Mystery
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 …
AlphaFold2 with ColabFold in Container
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 …
No GUI PyMOL – computing distances for thousands of PDB files from Rosetta
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 …
PyMOL and Biological Units from REMARK 350
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. …
New Tutorial Section: Computational Modeling
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 …
Rosetta Ligand Docking – Help with Docker
Summary Combine software and scripts on Docker and local macOS computer (Intel amd64 or arm64 Silicon Chip M series) to follow successfully the Rosetta tutorial Ligand Docking with a G-Protein Coupled Receptor. This method will …
POSE: build, manipulate, mutate, L, D, protein molecular structures
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 …
AlphaFold A practical guide Online Tutorial – EBI-EMBL
Summary This Free EBI/EMBL on-line course “AlphaFold, A practical guide” provides an understanding of the fundamental concepts behind AlphaFold2, how users can run protein predictions and integrate these predictions into their projects, and how AlphaFold2 …
3D Protein Imager a PyMOL/Qutemol web alternative
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 …