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Alexander Rose

@asrose.bsky.social
591 followers 594 following 23 posts

Scientific software engineer & computational structural biologist, #molstar web molecular graphics developer.

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Reposted by Alexander Rose
MDRepo @mdrepo.bsky.social · 17/08/2026
mdrepo.org now has its own account (that's me!) Follow the account for updates on content and functionality.
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Reposted by Alexander Rose
RCSB Protein Data Bank @rcsbpdb.bsky.social · 21/07/2026
Big PDB Changes Are One Year Away! On July 21, 2027, wwPDB will fully transition to extended PDB IDs for new depositions and the PDB archive will use a new directory structure based on 12-character extended PDB IDs. Visit wwpdb.org for details.
Be an Early Adopter: 
Transition to the new PDB Beta Archive, 
Extended PDB IDs, and PDBx/mmCIF File Format

The PDB Beta Archive contains all current PDB data and is updated weekly. Visit wwPDB.org for details.
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Alexander Rose @asrose.bsky.social · 24/06/2026
Beautiful and technically impressive work. Nice to see it highlighted.
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Reposted by Alexander Rose
corrylab.bsky.social @corrylab.bsky.social · 27/05/2026
Excited to share this paper from @yiechanglin.bsky.social showing how lipids can move between bacterial membranes along the bridge like protein TamB. Also happy to be able to post the cool movie. 🎥🌟 #MDsimulations #StructuralBiology doi.org/10.1016/j.bp...
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 16/05/2026
Try this new online training game from Leandro F. Estrozi designed for newcomers in structural biology, with a focus on cryo-EM and cryo-ET map interpretation: rico.ibs.fr/helixplo...
Screenshot of online game
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Reposted by Alexander Rose
RCSB Protein Data Bank @rcsbpdb.bsky.social · 28/04/2026
Explore PDB Structures in AR/VR RCSB PDB supports immersive Augmented Reality and Virtual Reality (VR) visualization within Mol*
rcsb.org
Explore PDB Structures in AR/VR
RCSB.org supports immersive Augmented Reality and Virtual Reality (VR) visualization within Mol*
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Reposted by Alexander Rose
Utz Ermel @uermel.bsky.social · 20/04/2026
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578
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Reposted by Alexander Rose
Ed Hutchinson @socialinfluenza.bsky.social · 17/04/2026
🚨New pre-print!🚨 Because influenza virions are highly variable in form no single method can show their molecular architecture in detail. Here, we integrate multiple structural and compositional approaches to identify new features of these beautiful virus particles www.biorxiv.org/content/10.6...
An illustration of an apical region of an animal cell in cross section, shown crowded with individual molecules. The plasma membrane is densely occupied by influenza virus glycoproteins, and from the surface bud influenza virions with different morphologies (L-R): spherical, bacilliform, filamentous with a genome, filamentous and empty, filamentous with a helical inner layer, and filamentous with a cofilactin cytoskeleton.
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Alexander Rose @asrose.bsky.social · 04/04/2026
latest #molstar publication pulling all details on its graphics engine together - lots of pretty pictures with Gianluca Tomasello (@proteinimaging.bsky.social), Áron Samuel Kovács, @ludovicautin.bsky.social, David Sehnal pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov
Mol* Web Molecular Graphics Engine
Web-based molecular graphics have transformed the interactive visualization of molecular data, leveraging modern web technologies that provide GPU acceleration, optimized JavaScript engines, and seamless access across devices without additional ...
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Alexander Rose @asrose.bsky.social · 03/04/2026
Trying some procedural animation for #molstar. Not real in any sense but intended to convey dynamics. github.com/molstar/mols...
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Reposted by Alexander Rose
Jan Stevens @janstevens.bsky.social · 13/02/2026
Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇
Cutaway and close-up views of a Martini coarse-grained whole-cell model of JCVI-syn3A, showing the densely packed cytoplasm with proteins, RNA, metabolites, and chromosome inside a lipid membrane with embedded membrane proteins
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 08/01/2026
Register for this January 26 webinar to learn what is new in the redesigned Advanced Search feature and how to use it go.rutgers.edu/ijwpxr1h
Register for the January 26 Webinar on Advanced Search
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Alexander Rose @asrose.bsky.social · 08/10/2025
Congrats to the 2025 #NobelPrize laureates in chemistry. Here are some #molstar renderings of an AgFe mixed metal Metal Organic Framework to celebrate.
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Alexander Rose @asrose.bsky.social · 06/10/2025
#molstar now supports immersive AR/VR - enjoy molstar.org/xr/
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 29/09/2025
Watch the Pairwise Alignment Tool Office Hour and learn how to align one or more protein chains to a reference structure in a pairwise manner
youtube.com
Introduction to RCSB PDB’s Pairwise Alignment Tool
The Pairwise Structure Alignment Tool (https://www.rcsb.org/alignment) can align one or more protein chains to a reference structure in a pairwise manner. This tool allows for simultaneous analysis and visualization of three-dimensional (3D) structure alignments and structure-based one-dimensional (
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 24/09/2025
MolViewSpec: describe, share, and reproduce Mol* molecular scenes with a simple extension
academic.oup.com
MolViewSpec: a Mol* extension for describing and sharing molecular visualizations
Abstract. Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broade
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 05/08/2025
Register for the Aug 11 Virtual Office Hour on Pairwise Alignment Learn how to align one or more protein chains to a reference structure in a pairwise manner pdb101.rcsb.org/news...
pdb101.rcsb.org
PDB101: Register for the Aug 11 Virtual Office Hour on Pairwise Alignment
PDB-101: Training, Outreach, and Education portal of RCSB PDB
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Reposted by Alexander Rose
Jochem Smit @jhsmit.bsky.social · 10/04/2025
New release for #ipymolstar: I've added a widget for the amazing and very powerful MolViewSpec. This allows you to control the camera📷from python🐍, as well as all other molviewspec features 🎉 ipymolstar repo: github.com/jhsmit/ipymo... Molviewspec: molstar.org/mol-view-spec/
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Reposted by Alexander Rose
Joachim Frank @joachim123.bsky.social · 17/03/2025
sorry, trying better res
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Alexander Rose @asrose.bsky.social · 18/01/2025
Isosurface of X-ray density only lit by emissive slice of same density. Illuminated in #molstar.
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Jochem Smit @jhsmit.bsky.social · 06/12/2024
You can try it on Huggingface: huggingface.co/spaces/Jhsmi... The data is only encoded in the link and not stored so you can use it to share unpublished data* (at your own risk, no warranty, links might stop working)
huggingface.co
Ipymolstar Annotate Colors - a Hugging Face Space by Jhsmit
Annotate protein structural models with colors
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Reposted by Alexander Rose
Jochem Smit @jhsmit.bsky.social · 06/12/2024
Here's a neat way to share you protein-annotated data 🚀🧪 Upload your .csv with residue/value data, select data column, colormap and norm to interactively color your protein model. Then, add title/description and click the button to open a shareable view with url-encoded data and settings.
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Brady Johnston @bradyajohnston.bsky.social · 01/12/2024
A quick molecule of the month render for November's Malaria Parasite PTEX (pdb101.rcsb.org/motm/299) using #b3d and #MolecularNodes #GeometryNodes #SciArt
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Jochem Smit @jhsmit.bsky.social · 29/11/2024
#ipymolstar v0.0.9: Added click interactions try it on pycafé: py.cafe/jhsmit/ipymo...
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Alexander Rose @asrose.bsky.social · 17/11/2024
Gave a short presentation on Illuminating Molecules in #molstar at the November 2024 #WebGL & #WebGPU Meetup www.khronos.org/events/webgl...
About Mol*

Suite of tools for 3D molecular data on the web
Custom WebGL rendering engine
Scales from single atoms to cells with billions

Wanted nicer lighting that still scales
“Path-traced” SSGI
Screen-space, so OK with billions of atoms
Sample-based, so good to adjust quality
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Brian Karis @briankaris.bsky.social · 15/11/2024
Significant new work on LOD of aggregates! mangosister.github.io/scene_agn_si...
mangosister.github.io
Efficient Scene Appearance Aggregation for Level-of-Detail Rendering
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Razvan Borza @rborza.bsky.social · 28/10/2024
🚀 Excited about our pre-print: AlphaBridge: A User-Friendly Tool for Interpreting Protein Predictions Whether you're an expert or just new to the field of Protein Prediction, AlphaBridge is the way to go! 🔁Try it and share your thoughts! 📜 Article: www.biorxiv.org/content/10.1...
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Diego del Alamo @delalamo.xyz · 08/11/2024
InterProt (interprot.com#/sae-viz/SAE...) is a tool that applies the same interpretability analysis used to make Golden Gate Claude to protein language models. For example feature 4000 recognizes residues lining inside of de novo designed & natural transmembrane beta-barrels (PDBs 6X1K, 6X9Z, 2MLH)
interprot.com
InterProt
Interpreting Proteins through Language Models
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Jochem Smit @jhsmit.bsky.social · 07/11/2024
Two-way tertiary/primary structure hover and highlight with #ipymolstar and #altair Try it on pycafe: py.cafe/jhsmit/ipymo...
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Alexander Rose @asrose.bsky.social · 26/10/2024
Ionic lock in inactive rhodopsin - illuminated in #molstar
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