RT @: Check out the new #PDB entries this week, 394 in total (http://www.ebi.ac.uk/pdbe/entry/search/index?document_type:latest_pdb&view=entry&sort=release_date+desc)!
Here is the crystal structure of the ScOAHS enzyme that catalyzes synthesis of l-methionine analogues (http://www.ebi.ac.uk/pdbe/entry/pdb/8OVH). This is a key step in developing new drugs. @EuropePMC_news

We must never forget that if #alphafold is so powerful, it is because the #AI was trained on the thousands of high quality experimental data of the #PDB to teach the #machinelearning #algorithm

I'm spending some time reversing a third party library in Python to understand the parsing process of a grammar on a translation experiment I'm working on. I've had to refresh my #PDB skills to understand how parameters are passed and what operations are being performed in the backstage.

Just in case it is useful for others, I've written a small but (I think) pretty simple article on how to use #PDB to debug #Python scripts bringing back some old notes. Check it here: https://github.com/febrezo/pdb-mini-tutorial

#Funfact #structuralbiology The #PDB code for the crystal structure of the active form of the MAP #kinase ERK2 is 2ERK 😬

https://www.rcsb.org/structure/2ERK

Breaking lines, mixing and matching stars and getting a feel from the players in camp/first few games led to the emergence of homegrown talent like #PaulCotter who is today CONFIDENTLY playing the 1st line in the absence of #JackEichel for today. #Cassidy also recognized that Stephenson could today move up to his natural position and so far that has paid off in faceoffs.

These are adjustments in roster utilization that #PDB would've never done with #VGK when they desperately needed them. 3/5

#VegasGoldenKnights roster aside, Cassidy was coming in with a fresh attitude, energy and goals for the team. In spite of him knowing what direction he wanted to go in, what I see with Cassidy is the polar opposite of #PDB. While PDB would force a system the players would have to mold to, Cassidy has built a system using the players strength and weaknesses. This has now balanced the roster in a way that is very similar to what made #Gallant successful at the helm for #VGK . 2/5

#AlphaFold predictions solve the #Crystallographic #PhaseProblem problem with an 85% success rate

(187 of 215 #PDB entries originally determined with experimental phasing automatically redetermined with iterative AlphaFold prediction and rebuilding)
https://www.biorxiv.org/content/10.1101/2022.11.18.517112v1
https://twitter.com/i/web/status/1594681582945595392

Hey Structural Biologists :protein:

#crystallography #MX #CryoEM #CryoET #NMR #SAXS #HDX #Alphafold #PDB #EMDB #StructuralBiology

I have created a group @strucbio .

If you tag this account in any relevant toot, it will automatically boost it.

So if you follow this account, any toots about structural biology should end up in your TL. The more people use it, the better it will be.

Boosting appreciated. :protein:

@terwilltom Thanks for posting this! Hope this will shape how we can best use the predictions from #AlphaFold. There is great information in those predictions, but definite need for caution. I like that the #PDB is including that info, but with clearly marked distinction btw experimental and computational. Thanks!
#StructuralBiology #AlphaFold

RT @PDBeurope@twitter.com

There are 364 new entries in the #PDB this week, including this structure of the mechanosensitive channel MscK from E. coli (7ux1), solved by #cryoEM and published in @NatureComms@twitter.com. View all new entries at http://pdbe.org/latest

🐦🔗: https://twitter.com/PDBeurope/status/1595348477101637633

#hardagree #moa
---
RT @terwilltom
#AlphaFold predictions solve the #Crystallographic #PhaseProblem problem with an 85% success rate

(187 of 215 #PDB entries originally determined with experimental phasing automatically redetermined with iterative AlphaFold prediction and rebuilding)
https://www.biorxiv.org/content/10.1101/2022.11.18.517112v1
https://twitter.com/TerwillTom/status/1594681582945595392

#AlphaFold predictions solve the #Crystallographic #PhaseProblem problem with an 85% success rate

(187 of 215 #PDB entries originally determined with experimental phasing automatically redetermined with iterative AlphaFold prediction and rebuilding)
https://www.biorxiv.org/content/10.1101/2022.11.18.517112v1

Partial structure of tyrosine hydroxylase in complex with dopamine showing the catalytic domain and an alpha-helix from the regulatory domain involved in dopamine binding.

https://www.rcsb.org/structure/6ZN2

#chemistry #protein #pdb #blender

@MirandaLynchPhD haha 😂I think you bring huge amounts of knowledge- no need for that course;) - it’s really to interest a few master students (German system, not yet signed up for grad school) from chemistry for biophysics and structure (we really started out from protein structure fundamentals… but I also introduced the #pdb #pymol #chimeraX in the first lecture, to make them explore protein structures along the way…

#TIL about the very useful 'interact' command in #Python #pdb that launches an interactive shell in the current scope. Don’t have to deal with prefixing custom statements with a ! or try to work around the limitations of a single-line prompt any more! In response, my colleague told me about the 'display' command to watch variables and expressions, when their values change. 😎

#forbes #science "AlphaFold Is The Most Important Achievement In AI—Ever" #AlphaFold #AI #DeepMind #BioInformatics #Protein #ProteinFold #PDB #ProteinDataBank #UniProt #OpenSource ... https://www.forbes.com/sites/robtoews/2021/10/03/alphafold-is-the-most-important-achievement-in-ai-ever/?sh=1faa4086e0af

#forbes #science "AlphaFold Is The Most Important Achievement In AI—Ever" #AlphaFold #AI #DeepMind #BioInformatics #Protein #ProteinFold #PDB #ProteinDataBank #UniProt #OpenSource ... https://www.forbes.com/sites/robtoews/2021/10/03/alphafold-is-the-most-important-achievement-in-ai-ever/?sh=1faa4086e0af

You won't believe me: for many, many years, I was debugging #Python (recreational, not professional!) with pure #pdb.
Yesterday evening, I tried #PuDB and now I can't wait to code anything just to be able to debug with this. 😁

#Checkliste für #Vim als #IDE für #Python

#Checkliste für die #Vervollständigung der #Datei #Vimrc

Bezüglich #Debugging sagt der Vortragende er benutze dafür nicht Vim, sondern #iPython und #ipdb (#IPython #pdb).

I will insert breakpoints with a shortkey, open another terminal window and start my program, waiting until the breakpoint is hit and then inspect the scope.

http://ipython.org/
https://pypi.org/project/ipdb/

https://youtu.be/YhqsjUUHj6g

RT @BioRender@twitter.com

Attn: Structural biologists, protein biochemists and those using the PDB!📣🔬We just launched a beautiful easy-to-use 3D shader for PDB molecules (#coronavirus spike protein shown here). It's available on the free version of @BioRender@twitter.com👨🏽‍💻👩🏻‍💻 Let us know your thoughts! #PDB #covid19

🐦🔗: https://twitter.com/BioRender/status/1235205778627342336