Biophysics; protein dynamics/folding using smFRET and HDX-MS. https://xitter.cf/t.co/nKLOvFw0xh
Leuven
Joined December 2012
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Jochem Smit retweeted
FRET correlation functions, a new model-free analysis tool. For dynamics from nano to milliseconds in diffusion-based smFRET experiments. Clean correlation functions, no diffusion component left. Perfect to verify HMM fits. biorxiv.org/cgi/content/shor…
Jochem Smit retweeted
Just out in time for Michele's viva tomorrow - his Magnum Opus (what a 4 month progress report can turn into!). Anything you ever didn't care to ask about HDX software is here - well almost 🙂 And good luck tomorrow morning for x-less Michele!
Jochem Smit retweeted
AnyWidget+Solara: How to build a basic widget with AnyWidget by @trevmanz in a Solara @solara_dev app
Jochem Smit retweeted
OPIG Postdoc Olly Crook (@OllyMCrook) has released the RexMS package for residue-level analysis of hydrogen deuterium exchange mass spectrometry (HDX-MS) data.
Read the preprint here: biorxiv.org/content/10.1101/…
And explore the codebase here:
ococrook.github.io/RexMS/
Jochem Smit retweeted
Also, if you want a fancy movie of the predicted states of your protein fold, i adapted the ColabFold implementation of ESMFold to do this in this notebook. Also #ChimeraX is needed
colab.research.google.com/dr…
Here are 3 examples with distincts folds. This is the Top7 fold :)
"Rendering protein mutation movies with MutAmore"
(gif below made from youtube.com/watch?v=1XgiFXg-…)
biorxiv.org/content/10.1101/…
github.com/kWeissenow/MutAmo…
Jochem Smit retweeted
💁PyHDX is python project which can be used to derive Gibbs free energy from HDX-MS data.
👉Check out the beautiful PyHDX app by @Jhsmit_ github.com/Jhsmit/PyHDX
#python #datascience #dataviz #Analytics #Chemistry
Jochem Smit retweeted
🚀 Introducing Solara a pure Python, React-style framework for scaling your web apps! Works with Jupyter Notebook, FastAPI, and more. Excited to hear your thoughts!
#Python #JupyterCon #ipywidgets
Jochem Smit retweeted
Really excited about ipyreact 😍
• Write jsx/tsx and it just works in Jupyter (no nodejs, webpack.. )
• Bi-directional communication browser ↔ Python
• Hot reloading of source files (thanks to AnyWidget @trevmanz )
• IPython cell magic %%react saves boilerplate
Jochem Smit retweeted
Just released #anywidget v0.2 ⚡ It brings modern web development to @ProjectJupyter:
- Automatic file loading 📂
- Integrated HMR 🔄
- Utility types for @typescript 🔒
- Dedicated API for custom cleanup logic 🧹
more info: anywidget.dev/blog/anywidget…
Jochem Smit retweeted
Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape #iScience cell.com/iscience/fulltext/S…
Jochem Smit retweeted
After 1.5 years of hard work, I am thrilled to share with you Φ-SO - a Physical Symbolic Optimization package that uses deep reinforcement learning to discover physical laws from data . Here is Φ-SO discovering the analytical expression of a damped harmonic oscillator👇
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Jochem Smit retweeted
What happens when a very smart and experienced LC expert gets ahold of your 'held together with duct tape' apparatus for millisecond HDX? Find out in this swanky new Analytical Chemistry paper: pubs.acs.org/doi/10.1021/acs…
Jochem Smit retweeted
Check out our new software for HDX-MS data analysis and visualization. The Deuterium Calculator: An Open-Source Tool for Hydrogen–Deuterium Exchange Mass Spectrometry Analysis pubs.acs.org/doi/10.1021/acs…
Jochem Smit retweeted
Additional postdoc positions available in strucural MS in Leeds (e.g. native/HDX). Please RT, if interested DM me
Jochem Smit retweeted
PhD studentship available in our group in Manchester, please get in touch for info: findaphd.com/phds/project/mr…
Jochem Smit retweeted
Want to build interactive #cheminformatics apps using #python that can be deployed to github pages? NO SERVER REQUIRED.
You can now with @Panel_org 0.14 and PANEL-CHEMISTRY 0.2.1.
$ pip install panel-chemistry
Check out github.com/awesome-panel/pan…
#chemistry #dataviz #datascience
Jochem Smit retweeted
Doing multicolor (single-molecule) imaging? Tired of waiting for each color?
Want simultaneous imaging with full field of view but without the multicamera hassle?
Take a look at our 'Circulator'! 🔥💪
t.ly/lHZq. Very excited so please RT! (1 of 5)
#microscopy
Jochem Smit retweeted
Evolutionary adaptation of the protein folding pathway for secretability - from comparing slow-folding secreted bacterial protein PpiA and its fast-folding cytosolic homologue PpiB
Anastassios Economou, Spyridoula Karamanou and coworkers @KU_Leuven
embopress.org/doi/10.15252/e…
