@Jhsmit_

Biophysics; protein dynamics/folding using smFRET and HDX-MS. https://xitter.cf/t.co/nKLOvFw0xh

 Leuven
jhsmit.org
Joined December 2012
  • Tweets255
  • Following478
  • Followers224
32Media
New feature in #ipymolstar v0.0.7: You can now use the mouseover event to highlight protein residues bidirectionally between #altair charts. In this example the colors represent PyHDX derived #hdxms ΔG's (roughly local flexibility)
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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…
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Code available on @py_cafe: py.cafe/jhsmit/ipymolstar-al… This is using altair's JupyterChart which works really well if you want to get selections with python. You can't set selections yet, so I'm 'manually' setting the x-pos of the line. Is there a better way? #anywidget @vega_vis
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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!
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You can now use ipymolstar in panel apps 🥳 ipymolstar v0.0.6 adds panel's AnyWidgetComponent so you can interact with the PDBeMolstar widget directly from panel/python🐍 @Panel_org @MarcSkovMadsen @PhilippJFR
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There is a live example on @py_cafe: app.py.cafe/jhsmit/ipymolsta…

PyCafe - Panel - Molecular Structure Coloring Interface

Create & Share Streamlit, Dash and Python Apps Online.

app.py.cafe
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By popular demand: How much monomer/dimer/tetramer are formed at steady-state given the two kds and the total concentration of protomer? 🧐 py.cafe/jhsmit/tetramerizati…
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Here is another fun one over on @py_cafe ☕️ Protein residue coloring in ipymolstar is now super fast with the latest PDBeMolstar version. Makes for very responsive protein viewer apps! And supports dark mode 😎
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forgot step 3. share the link: 😅 py.cafe/jhsmit/ipymolstar-ra…
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Super excited to announce the pre-release of @py_cafe 🎉 py.cafe is a platform that lets you create, run, edit, and share Python (web) applications directly in your browser. No installation is needed—just a single click, and it runs! #Python #pyodide 🧵👇🏻

PyCafe: Create & Share Streamlit, Dash and Python Apps Online.

Playground for Python web frameworks. Run and edit Python code snippets for web frameworks in a web browser.

py.cafe
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We have several positions open in our lab ! 📢🥳 Check our tweet feed !
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#alphafold3 is incredible! I've created this #solara app where you can drag & drop your result .zip file and switch between chain color or plddt colors. Includes 'spin' and theme toggle for maximal viewing pleasure. The video below shows the elusive SecA2/SecB4 complex.
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link to huggingface space: huggingface.co/spaces/Jhsmit… With PDBeMolstar 0.3.2 / ipymolstar 0.0.5 you can also set custom tooltips. Neat!
screenshot of ipymolstar viewer with custom tooltip

ALT screenshot of ipymolstar viewer with custom tooltip

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AnyWidget+Solara: How to build a basic widget with AnyWidget by @trevmanz in a Solara @solara_dev app
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New in #ipymolstar version 0.0.4: directly load your local data files `pip install "ipymolstar==0.0.4"` github.com/Jhsmit/ipymolstar
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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/

Inferring residue level hydrogen deuterium exchange with ReX

Hydrogen-Deuterium Exchange Mass-Spectrometry (HDX-MS) has emerged as a powerful technique to explore the conformational dynamics of proteins and protein complexes in solution. The bottom-up approach...

biorxiv.org
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I've created my first widget with #anywidget! Its called `ipymolstar` and allows visualization of proteins or molecules interactively from python check out the video below where I'm using ipymolstar in a @solara_dev app or try the live demo on ploomber: purple-glade-1760.ploomberap…
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ipymolstar uses Mol* via the PDBeMolstar implementation. Current release is v0.0.3 where most basic functionality is implemented. Mouseover events from js to python are next on the list! @maartenbreddels @trevmanz @asrmoin @ploomber
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.. and dark mode is also supported!
screenshot of ipymolstar solara app in dark mode

ALT screenshot of ipymolstar solara app in dark mode

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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 :)
Diego del Alamo@DdelAlamo18 Sep 2023
"Rendering protein mutation movies with MutAmore" (gif below made from youtube.com/watch?v=1XgiFXg-…) biorxiv.org/content/10.1101/… github.com/kWeissenow/MutAmo…
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