Using X-ray crystallography at the Advanced Light Source (ALS), research scientist Banumathi Sankaran at the Berkeley Center for Structural Biology (BCSB) has helped confirm the successful design of proteins that toggle between two different shapes in response to biological triggers.

Read more: https://biosciences.lbl.gov/2023/08/29/bcsb-confirms-design-of-stimulus-responsive-two-state-proteins/

Berkeley Lab #ProteinDesign #MachineLearning #StructuralBiology #Science #RoseTTAFold #ProteinMPNN #AlphaFold2

#Symbiotic and #pathogenic #fungi may use similar molecular tools to manipulate #plants.

#mycorrhiza #AlphaFold2 #AI #Rhizophagus #MycFOLDs

https://phys.org/news/2023-06-symbiotic-pathogenic-fungi-similar-molecular.html

Reading #AlphaFold2 and #OMSF #OpenFold code is great but with #protein #molecules in your hands you feel it better. Designing the kit in #FreeCAD ensures you know bond lengths and angles etc. So I spent few days learning and printing. The kit is optimized for protein #folding, single bond rotates but can be fixed in #peptide bond, it keeps shape even before adding #hydrogen #bonds in #alphahelix (or pair #RNA bases by H-bond).

Print your #kit and enjoy #biochemistry!

https://www.printables.com/model/457984-molecules-for-protein-folding

Im Kielwasser von #AlphaFold2 jagt gegenwärtig ein Programm zur Vorhersage von #Protein­strukturen das nächste. Was müssen sie mitbringen, um auch die Mechanismen der Proteinfaltung zu enträtseln? …

— Henrik Müller gibt Antworten: 👉 https://www.laborjournal.de/rubric/methoden/methoden/v276.php

Great to see this collaborative effort spearheaded by Michaela Reissland from http://diefenbacher-lab.com/ out as #preprint 📝

Stabilisation of β-Catenin-WNT signalling by USP10 in APC-truncated colorectal cancer drives cancer stemness and enables super-competitor signalling

https://www.biorxiv.org/content/10.1101/2023.02.10.527983v1

#peptide microarray studies in our lab and #AlphaFold2 Multimer provided insights into β-catenin - USP10 binding in single amino acid resolution. Huge thx to all co-authors! 👏 #cancer #research

Hallvard Olsvik & @TerjeJohansen17 explore a new #PLOSBiology study showing how the AI-based tool #AlphaFold2-multimer can be used to identify sequence motifs that bind to the ATG8 family of #autophagy proteins. Paper: https://plos.io/3YDtLIM Primer: https://plos.io/40TgKwG

#Alphafold2-multimer assisted prediction of typical & atypical ATG8-binding motifs enables fast-forward discovery of #autophagy modulators, including the central autophagy regulator ATG3 @TarhanEI @BubeckLab @Tolga_Bzkrt &co #PLOSBiology https://plos.io/3YDtLIM

Hallvard Olsvik & @TerjeJohansen17 explore a new #PLOSBiology study showing how the AI-based tool #AlphaFold2-multimer can be used to identify sequence motifs that bind to the ATG8 family of #autophagy proteins. Paper: https://plos.io/3YDtLIM Primer: https://plos.io/40TgKwG

#Alphafold2-multimer assisted prediction of typical & atypical ATG8-binding motifs enables fast-forward discovery of #autophagy modulators, including the central autophagy regulator ATG3 @TarhanEI @BubeckLab @Tolga_Bzkrt &co #PLOSBiology https://plos.io/3YDtLIM

Hallvard Olsvik & @TerjeJohansen17 explore a new #PLOSBiology study showing how the AI-based tool #AlphaFold2-multimer can be used to identify sequence motifs that bind to the ATG8 family of #autophagy proteins. Paper: https://plos.io/3YDtLIM Primer: https://plos.io/40TgKwG

RT @TarhanEI
Officially out in @PLOSBiology!! Take a look at how we are accelerating our research with AI @DeepMind #AlphaFold2 https://twitter.com/PLOSBiology/status/1623622070226632705

@holeungng I think this paper makes a strong case for using perturbation analysis like adversarial attacks to test for the robustness of protein folding neural networks (PFNNs). They conclude AF2 is not robust enough yet to say that the protein fold prediction problem has been solved. #AlphaFold2 #AI

A fehérjék szekvenciájából 3D szerkezeteket előállító #AlphaFold2 2020-ban megoldotta a molekuláris biológia egyik legnagyobb problémáját.

Az algoritmusok legújabb versenyén az is körvonalazódott, hogy merre halad tovább a terület. #AI

- erről is írtam a héten:

https://qubit.hu/2023/01/12/elkepesztoen-fejlett-feherjekutato-algoritmusok-versengenek-egymassal-hogy-felterkepezzek-a-legalapvetobb-biologiai-folyamatokat

👀 #Preprint @strucbio
#AlphaFold2 can predict #structural and #phenotypic effects of #single #mutations https://www.biorxiv.org/content/10.1101/2022.04.14.488301v2

More notes from the #CASP15 competition. Other resources here: https://www.aditiashenoy.com/posts/casp15/day2/

RT @AlbertVilella@twitter.com

Some initial results from the #CASP15 competition and we see that #Alphafold2 has become a fertile ground for experimentation by several research groups around the world. Facebook's ESM protein language models (pLMs) are the top non-MSA based methods.

🐦🔗: https://twitter.com/AlbertVilella/status/1601909663309901824

Standing on the shoulders of giant neural networks :)

RT @AlbertVilella@twitter.com

Some initial results from the #CASP15 competition and we see that #Alphafold2 has become a fertile ground for experimentation by several research groups around the world. Facebook's ESM protein language models (pLMs) are the top non-MSA based methods.

🐦🔗: https://twitter.com/AlbertVilella/status/1601909663309901824

last week to apply!

RT @gem__atkinson@twitter.com

Do you love structural #bioinformatics? Would you like to be based in a beautiful city & region, working with colleagues to make exciting new discoveries? Consider joining us in Lund University https://lu.varbi.com/en/what:job/jobID:564808/
#structuralbiology #alphafold2 #alphafold #AI
Please share!

🐦🔗: https://twitter.com/gem__atkinson/status/1598234355859881984

***One week left to apply!***
Do you love structural #bioinformatics? Would you like to be based in a beautiful city & region, working with colleagues to make exciting new discoveries? Consider joining us in Lund University https://lu.varbi.com/en/what:job/jobID:564808/
#structuralbiology #alphafold2 #alphafold #AI #cryoEM #computationalbiology
Please share!

This looks useful for generating alternative conformations of various classes of proteins for drug design.

Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties

#DrugDesign #StrucuralBiology @strucbio #science #AlphaFold2
http://biorxiv.org/cgi/content/short/2022.12.11.519936v1?rss=1

RT @AlbertVilella@twitter.com

Some initial results from the #CASP15 competition and we see that #Alphafold2 has become a fertile ground for experimentation by several research groups around the world. Facebook's ESM protein language models (pLMs) are the top non-MSA based methods.

🐦🔗: https://twitter.com/AlbertVilella/status/1601909663309901824