Gabriel Axel

MLCB24 - Machine Learning in Computational Biology Fall 2024 - YouTube Manolis Kellis + Eric Alm

Course by Manolis Kellis: www.youtube.com/playlist?lis...

Seminars about specific cases from Narayan Lab, University of Michigan: www.youtube.com/@narayanlabu... and Boston Protein Design and Modeling Club: www.youtube.com/@bpdmc

I suppose this is an inherent issue of any learning-based tool that doesn't actually perform energy calculations. Maybe an additional step for that can be added, similar to how ColabFold has an AMBER relaxation option? It would still be faster than classical docking/MD overall.

The specificity of cytokinin signalling in Arabidopsis thaliana is mediated by differing ligand affinities and expression profiles of the receptors Arabidopsis thaliana has three membrane-located cytokinin receptors (AHK2, AHK3 and CRE1/AHK4), which are sensor histidine kinases containing a ligand-binding CHASE domain. Despite their structural ...

Marvelous! I tried to use Boltz-2 to compare the binding affinities of different cytokinins to CHASE domain, the results were mostly in line with existing work (doi.org/10.1111/j.13...), except for cis and trans zeatin the predicted affinities were similar while expected to differ significantly.

I experienced a similar exertion. I think an important question to ask is whether they are interested in developing new computational methods (i.e. "the next AlphaFold"), or implementing, modifying and assembling existing (and future) computational methods to answer specific biological questions.

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Maybe neurosnap.ai

Computational Structural Biology - YouTube

I should post something. Here are a few tutorial videos I made for the structural biology classes I give. I hope they will be useful to someone. Feel free to suggest more topics that you would like to see in future videos. 🖥️🧬🧶 www.youtube.com/playlist?lis...