My PhD research proposal is nearly done after over a month of working on it full tilt. Been an incredible (re)learning experience! Feel so much more comfortable with producing academic style writing again. Had some mega size cobwebs to dust off there. 🕸 Helps to have had to read so many journal articles to grok it all and connect the dots.
Excited to start reaching out to programs and lab heads! :neofox_glasses: If you happen know folks here on mastodon that are involved in Computational Biology or Biophysics program please drop names in replies or boost for reach. Looking to connect!
Now to treat myself to a much needed rest day and massage for my keyboard-warped back and tired eyed. ♨️
#research #compBio #proteinStructure #molecularDynamics #bioPhysics
#ProteinStructure
💊 Can understanding receptor bias help us design safer, more selective GPCR drugs?
🔗 Biased activation of the vasopressin V2 receptor probed by molecular dynamics simulations, NMR and pharmacological studies. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.10.039
📚 CSBJ: https://www.csbj.org/
#GPCR #StructuralBiology #MolecularDynamics #NMR #Pharmacology #ProteinStructure #DrugDiscovery #ComputationalBiology #CellSignaling
🧫 What secret molecular choreograph helps bacteria stay resilient against antibiotics and detergents?
🔗 Coordinated subdomain movements of MlaC regulate ligand binding and transport. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.031
📚 CSBJ: https://www.csbj.org/
#Microbiology #AntibioticResistance #MembraneBiology #StructuralBiology #ComputationalChemistry #MolecularDynamics #ComputationalBiology #Biophysics #ProteinStructure #DrugDiscovery #MolecularDocking
16-Sep-2025
Better understanding of #bitter #taste receptors: An AlphaFold3-based structure study
Researchers use an advanced AI-based prediction model, #AlphaFold 3, to predict the structure of human bitter taste #receptors
https://www.eurekalert.org/news-releases/1098406
🌀 Could a protein that twists into filaments reveal how cells keep themselves in balance?
🔗 Cryo-EM structure of AAA + ATPase thorase reveals novel helical filament formation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.018
📚 CSBJ: https://www.csbj.org/
#StructuralBiology #CryoEM #Thorase #MolecularBiology #mTORC1 #ProteinStructure #Biophysics #AAAplusATPase #SynapticPlasticity #Mitochondria
Sometimes while reading scientific articles I feel like they just slammed the keyboard randomly.
I am excited to introduce our new @EvolLetters paper that has just come out:
https://academic.oup.com/evlett/advance-article/doi/10.1093/evlett/qraf026/8223096
🧵1/7
#temperature #adaptation #enzyme #microbes #ProteinStructure
🪨 Can sand-like molecules help us map the secrets of protein structure?
🔗 Adsorption of silica oligomers on biomolecules: Structural and dynamical insights for atom probe tomography via classic molecular dynamics simulations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.004
📚 CSBJ: https://www.csbj.org/
#AtomProbeTomography #MolecularDynamics #Biophysics #ProteinStructure #Nanotech #ComputationalBiology #StructuralBiology #Biomaterials #ProteinScience
🧩 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`
🧠 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
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
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