Brute force simulations.

"These proteins should form a pore through which RNA can pass."

Me: Manually places the RNA in the middle of the proteins on a membrane and hopes for a miracle (or a pore).

#compchem #simulation #moleculardynamics #proteinStructure #rna #protein #academicchatter #chemistry #pymol

My protein does not feel well.

#compchem #model #protein #pymol

The claim "PyMOL-RS is a clean-room rewrite" of #PyMol, at https://github.com/zmactep/pymol-rs is clearly wrong.

The Rust code refers to PyMol filenames and function names. It has code structurally similar to PyMol's. It contains comments like "This is a faithful port of PyMOL's `ccealignmodule.cpp`" -- with quoted PyMol source code!

This comes across like yet another case of license and credit laundering using modern code generation tools. The author has not responded to me at https://news.ycombinator.com/item?id=47164180 .

🧬 Can we turn evolutionary signatures into maps of protein function?

🔗 Analysis of Fbox substrate adapter proteins using ProteoSync, a program for projection of evolutionary conservation onto protein atomic coordinates. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.09.012

📚 CSBJ: https://www.csbj.org/

#ProteinScience #StructuralBiology #ProteoSync #ComputationalBiology #Bioinformatics #EvolutionaryBiology #MolecularBiology #PyMOL

Oh man. Ich weiß auch nicht, warum die Betreuung von Promovierenden so viel Spaß macht.

Aber das gemeinsame Brainstorming und Probleme lösen, das fetzt einfach total.

Hat alles voll die Sogwirkung. Und mit jedem Paper und weiteren Tool tut sich direkt ein neues Rabbit Hole auf. 😅😂🫣

Aktuell betreue ich eine Doktorandin, die Proteinsimulation macht.

#Gromacs #Alphafold #PyMOL

PyMOL設定小ネタ
https://qiita.com/Ag_smith/items/bef5648928229f862649?utm_campaign=popular_items&utm_medium=feed&utm_source=popular_items

#qiita #pymol

Working on #scientificPython visualization tools for molecular biology?

Submit your proposal to #EuroSciPy2025 and demonstrate your advances in interactive 3D rendering, protein structure analysis, or molecular dynamics visualization!

CfP: https://pretalx.com/euroscipy-2025/cfp

#PyMol #EuroSciPy

#OpenSource multicolor #3Dprinted #molecular #orbital models for a 1st semester organic #chemistry course:

- #classroom-acessible MO theory
- transition state understanding
- #PyMOL- / #Blender-exported .stl files

https://doi.org/10.1021/acs.jchemed.4c00945
#DIYchem #lab #tools #education #CompChem #STEM #Chemie #Schule #MINT