🧩 What happens when we put AlphaFold2’s predictions to the ultimate test—across species and structure types?

🔗 Comprehensive assessment of AlphaFold’s predictions of secondary structure and solvent accessibility at the amino acid-level in eukaryotic, bacterial and archaeal proteins. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.047

📚 CSBJ: https://www.csbj.org/

#AlphaFold #Bioinformatics #StructuralBiology #AlphaFold2 #ProteinStructure #ProteinPrediction #AI

🧬 How do AlphaFold2 and ESMFold stack up when it comes to functional annotation?

🔗 AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.01.008

📚 CSBJ: https://www.csbj.org/

#AlphaFold2 #ESMFold #AIinScience #ProteinStructure #Enzymes #Pfam #UniProt #AlphaFold #HumanProteome #FunctionalAnnotation #AIinBiology #ComputationalBiology #FunctionalGenomics

`Recent research highlights the transition from a pathological to a functional perspective of amyloid fibrils, paving the way for innovative applications in biotechnology and materials science. By leveraging the self-assembly properties and biocompatibility of functional amyloids, advancements in drug delivery, tissue engineering, and nanotechnology are emerging`

https://arxiv.org/abs/2504.15532

#proteinStructure #betaSheet

🧠 Can post-processing and deep learning push protein prediction to near perfection?

🔗 Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings. DOI: https://doi.org/10.1016/j.csbj.2024.12.022

📚 CSBJ: https://www.csbj.org/

#DeepLearning #Proteins #PSSP #ProteinStructure #ProtBERT #CNN #AlphaFold #AI #Proteomics

The third lecture by Dr. Ali Hassanali from the Abdus Salam International Centre for Theoretical Physics (ICTP) is on Enabla! In this one, Ali highlights the importance of energy transformations -- specifically electronic, mechanical, and thermal energies -- that are crucial for processes like protein folding and enzymatic reactions. Additionally, Dr. Hassanali outlines the hierarchical structure of proteins and the significance of dihedral angles in defining their secondary structures.

📚 This is a fantastic opportunity not only to learn but also to engage in discussions! You can access the lecture for free and ask your questions directly to Dr. Hassanali and other Enabla users online at https://enabla.com/pub/1163/about

#Nanotechnology #Biophysics #ProteinStructure #EnergyInteractions #OpenAccess

📝 Call for Papers: Special Issue on "Mechanistic insights into membrane protein dynamics and allostery: implications in drug discovery"

🔗Link to the 'Call for Papers': https://www.csbj.org/allostery

📊 Guest Editor:

🌟Prithviraj Nandigrami, Albert Einstein College of Medicine, USA

#membraneproteins #proteindynamics #proteinstructure #drugdiscovery #transmembranesignaling #molecularsimulation #therapeuticmolecules

DEADLINE EXTENDED: The new deadline for submission of manuscripts for this special issue is 31 January 2025.

📝 Call for Papers: Special Issue on "AlphaFold in Protein Structure and Function Prediction".

🔗Link to the 'Call for Papers': https://www.csbj.org/call_AlphaFold

📊 Guest Editors:

🌟Lukasz Kurgan, Virginia Commonwealth University, United States of America
🌟Jianyi Yang, Shandong University, China

#AlphaFold #ProteinStructure #ProteinFunction #DrugDesign #TargetPrediction

I was a beta tester for the Nobel prize-winning AlphaFold AI – it’s going to revolutionise health research
#AI #Chemistry #Health #AlphaFold #NobelPrize #HealthResearch #ProteinStructure #Biotechnology #DrugDiscovery #AIinScience #MolecularBiology
https://the-14.com/i-was-a-beta-tester-for-the-nobel-prize-winning-alphafold-ai-its-going-to-revolutionise-health-research/

Some exciting #glycotime to start the week!

GlycoShape is fresh off the press today on Nature Methods https://www.nature.com/articles/s41592-024-02464-7 :awesome:

Check out the short thread below 1/6

#Science #ProteinStructure #glycobiology

2024 Nobel in Chemistry for “Designing protein” and “Predicting protein structure”  
One half of the Nobel Prize in Chemistry 2024 has been awarded to David Baker “for computational protein design”............
#AImodel #AlphaFold2 #Aminoacids #DavidBaker #DemisHassabis #JohnJumper #NobelPrizeinChemistry #PROTEIN #Proteindesign #Proteinstructure
SC

https://www.scientificeuropean.co.uk/sciences/chemistry/2024-nobel-in-chemistry-for-designing-protein-and-predicting-protein-structure/

Wow 🤯 - my former post doc advisor David Baker won the Nobel Prize for Protein Design. Huge congrats - well deserved! David and his lab have been a force of nature in protein design. Incredible watching the progress over the last 20 years. #NobelPrize2024 #proteindesign #ProteinStructure

AI-powered protein structure prediction has revolutionized our field. The Nobel Prize in Chemistry was awarded to Baker, Hassabis, and Jumper for their groundbreaking work, propelling Medicine, BioTech, and AgriTech forward.
This technology complements traditional methods, enhancing our understanding of protein structure and function. The Nobel recognition underscores the impact of computational approaches in structural biology. Exciting times ahead!
#nobelprizechemistry
#AI
#ProteinStructure

Elizabeth Villa's lab delivers big time again with in-cell cryo-electron tomography of the nuclear pore complex:

"The molecular architecture of the nuclear basket" by Singh et al. 2024.
https://www.cell.com/cell/fulltext/S0092-8674(24)00780-3

#CellBiology #CryoEM #ProteinStructure #StructuralBiology

From the annals of Alphafold surfing, I was looking at some yeast-specific genes in preparation for a talk that will feature what you can learn by studying yeast-specific genes.

Look at this beauty:

ECM33-somehow involved in glucose uptake, extracellular GPI anchored protein.
#AlphaFold #StructuralBiology #ProteinStructure

AlphaFold 3 is out but... https://macinchem.org/2024/05/10/alphafold-3-is-out-but/ #ArtificialIntelligence #proteinstructure
#compchem

AlphaFold3 is now available and looks like it can handle all molecule interactions!

Webserver: https://golgi.sandbox.google.com/about
Paper: https://www.nature.com/articles/s41586-024-07487-w

#AlphaFold #AlphaFold3 #ProteinStructure

Just Published

Advanced Technologies for Protein Complex Production and Characterization. Volume II.

https://link.springer.com/book/10.1007/978-3-031-52193-5

This edited volume discusses the identification, discovery, characterization, structure determination and modeling of multicomponent macromolecular complexes.

The first volume (https://link.springer.com/book/10.1007/978-3-319-27216-0), targeted methods of recombinant production of protein complexes.

Enjoy!

#ProteinComplexes #Biochemistry #ExpressionSystems #Protein #ProteinStructure #SystemsBiology

Unlocking the Mysteries of Protein Structure: Coiling and Supercoiling

#AlphaHelices, #BetaSheets, #Protein, #ProteinCoiling, #ProteinStructure, #ProteinSuperCoiling, #TertiaryStructure #Biochemistry Proteins are the workhorses of life, orchestrating countless biological processes within cells. Their functionality is intimately tied to their structure, which can range from simple linear chains to intricate three-dimensional shapes.…. Medical Microbiology & Recombinant…

https://micrordt.wordpress.com/2024/04/27/unlocking-the-mysteries-of-protein-structure-coiling-and-supercoiling/

✨ @SWISS_MODEL has a fresh new logo!

It evokes four globular chains of interacting proteins, as #SWISS-MODEL allows to model protein complexes in 3D. Discover this leading #ProteinStructure homology-modelling platform, one of the 14 leading Open Science bioinformatics resources developed by our teams to serve millions of scientists.

SIB provides support to enhance brand visibility of its resources alongside UX, data protection...

👉 Read more: https://www.sib.swiss/services/open-software-and-databases

#ProteinModeling

@cmdcolin

I use Alphafold (actually colabfold) and am happy to answer questions, but I'm just a user. There are people with more expertise than me here.

Hashtags might find the right people

#StructurePrediction #alphafold #alphafold2 #colabfold #ProteinStructure #StructuralBiology #ProteinPrediction #protein #bioinformatics