CSBJOct 31

🧬 Can AI build peptides that tell your cells to fight back against oxidative stress?

🔗 RoseTTAFold diffusion-guided short peptide design: a case study of binders against Keap1/Nrf2. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.02.032

📚 CSBJ: https://www.csbj.org/

#StructuralBiology #PeptideTherapeutics #RoseTTAFold #ProteinEngineering #MolecularDynamics #AIinDrugDiscovery #AntioxidantResearch #DrugDesign #Bioinformatics #ComputationalBiology

Show threadJanGebauerMay 13, 2024
@xtaldave @strucbio I always had the feeling #AF2 was published because of #RosettaFold.... But surely nobody knows for sure 😉
eliza-ngMay 9, 2024
🔬 Exciting showdown alert! 🌟 Dive into the world of protein structure prediction with #RosettaFold All Atom vs. #AlphaFold - two powerhouses revolutionizing the field. 🧬
https://www.eliza-ng.me/post/sidentifiedfrom_4/
#ProteinPrediction #Bioinformatics #BlogPost
The Protein Prediction Showdown: RosettaFold All Atom vs. AlphaFold - Breaking Boundaries in Protein Structure Prediction

A new protein structure prediction model released by David Baker’s laboratory is making waves in the scientific community, challenging the dominance of DeepMind’s AlphaFold. The model, named RosettaFold All Atom, not only predicts protein structures but also incorporates bound DNA and ligands. What sets this model apart is its open-source nature, allowing for greater accessibility and collaboration within the scientific community. The rivalry between DeepMind’s AlphaFold and Baker’s laboratory model adds an exciting dynamic to the field of protein structure prediction.

Musings by Eliza Ng
CellBioNewsMar 11, 2024

Scientists develop #deep_learning method to design #bilin_binding #proteins.

#AI #RoseTTAFold

https://phys.org/news/2024-03-scientists-deep-method-bilin-proteins.html

Scientists develop deep learning method to design bilin-binding proteins

David Baker's group at the University of Washington, Seattle, U.S., have developed a novel deep learning method, RoseTTAFold All-Atom (RFAA), for prediction and design of complexes of proteins, small molecules, and nucleic acids. Subsequently, they developed RFdiffusionAA, which builds protein structures around small molecules.

Phys.org
JanGebauerDec 6, 2023
First session over at #EMBOComp3D - was very nice to hear John Jumper and @minkbaek talking about #AlphaFold and #RosettaFold next to each other. It's vitally important to have two methods challenging each other - this is essentially how science works. Kudos two both teams!
JanGebauerNov 1, 2023
#Alphafold might be getting much better in ligand binding prediction https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/ - sounds similar to #RoseTTAFold AA (#RFAA) https://www.biorxiv.org/content/10.1101/2023.10.09.561603v1 can't wait to get both on my hands... 😀 @strucbio #StructuralBiology
A glimpse of the next generation of AlphaFold

Progress update: Our latest AlphaFold model shows significantly improved accuracy and expands coverage beyond proteins to other biological molecules, including ligands.

Google DeepMind
LBNL BioSciAug 30, 2023

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

BCSB Confirms Design of Stimulus-responsive, Two-state Proteins - Biosciences Area

AI-generated hinge proteins could open the door to solving complex challenges in the world of protein design.

Biosciences Area
ℵ₀ 🏳️‍⚧️🏴‍☠️Jul 12, 2023

https://www.nature.com/articles/d41586-023-02227-y
↓
https://www.nature.com/articles/d41586-023-02227-y.pdf
;
↓
https://www.nature.com/articles/s41586-023-06415-8
#preprint #proteindesign #biology #nature #rosettafold #diffusion #rfdiffusion
;
https://www.biorxiv.org/content/10.1101/2022.12.09.519842v2

https://github.com/RosettaCommons/RFdiffusion
#github

AI tools are designing entirely new proteins that could transform medicine

Digital art techniques can now devise custom, working biomolecules on demand.

Fɹancisco J Яodríguez AmorínJun 26, 2023

“Nuestros programas de diseño de proteínas están abiertos y los usan investigadores en todo el mundo”.
#DavidBaker, creador de la herramienta #RoseTTAFold.
#AgenciaSINC
#INNOVACIÓN
#Ciencia
https://www.agenciasinc.es/Entrevistas/Nuestros-programas-de-diseno-de-proteinas-estan-abiertos-y-los-usan-investigadores-en-todo-el-mundo

Más en
https://rodriguezamorin.blogspot.com/p/radios.html?#Ciencia

“Nuestros programas de diseño de proteínas están abiertos y los usan investigadores en todo el mundo”

El laboratorio de este bioquímico en la Universidad de Washington ha desarrollado una vacuna contra la covid-19 y tiene en marcha un espray nasal que bloquea virus respiratorios. Además, está trabajando en inmunoterapia del cáncer y catálisis para la descomposición de moléculas tóxicas en el medio ambiente, entre otras aplicaciones. Todas ellas se basan en proteínas sintéticas creadas mediante inteligencia artificial de aprendizaje profundo.

Agencia SINC
Antoine TalyJun 12, 2023

A new perspective paper in JCIM "Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology" written with Marc Graille and
@sacquin_mo to explore how #AlphaFold, #RosettaFold, #EsmFold have modified the field of X-ray crystallography

https://doi.org/10.1021/acs.jcim.3c00381