Dwendscheck (dwendscheck.bsky.social)

AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly biorxiv.org/content/10.110… --- #proteomics #prot-preprint

Protenix - Yet another reproduction of AF3 github.com/bytedance/Prot…

PhD and Postdoc Positions in Data-Driven Simulation and Digital Twins @sanja_kit jobrxiv.org/job/karlsruhe-… #data_science #digital_signal_processing #modeling #simulation #ScienceJobs #job jobrxiv.org/job/karlsruhe-…

Our team is looking for a Post Masters Research Assistant! If you're interested in doing some really cutting edge Mass Spectrometry Imaging and Method Development, please apply! @PNNLab @asmsnews @IMSSNews careers.pnnl.gov/jobs/9932?lang…

Spatial proteomics of single cells and organelles on tissue slides using filter-aided expansion proteomics nature.com/articles/s4146… --- #proteomics #prot-paper

@CellReports "Pepties" (graphical abstract)🧐

Deciphering the regulatory mechanisms and biological implications of ARID1A missense mutations in cancer dlvr.it/TFtMK2

⚠️Here’s yet another option other than BioRender! ⚠️ 📢 SciDraw is a free repository of high quality drawings of animals, scientific setups, and anything that might be useful for scientific presentations and posters. 🔁❤️Free Science! RIP BioRender!!

Timescales in Cell Biology

AlphaBridge: tools for the analysis of predicted macromolecular complexes • AlphaBridge introduces tools to analyze and visualize the interfaces between predicted macromolecular complexes using data from AlphaFold3. It processes the predicted interactions into intuitive diagrams and 3D models for easy interpretation. • The tool uses a novel “Predicted Merged Confidence” (PMC) matrix, which combines the Predicted Local Distance Difference Test (pLDDT) and Predicted Aligned Error (PAE) metrics to identify multi-component structural modules and binary interfaces with high confidence. • AlphaBridge uses graph-based community clustering to detect interaction motifs in biomolecular complexes, then visualizes these interactions as chord diagrams (“AlphaBridge diagrams”) to provide a clear and intuitive summary of predicted binding interfaces. • The tool allows researchers to evaluate the reliability of interactions in predicted protein-protein, protein-DNA, and protein-RNA complexes, offering a scoring and ranking system for predicted interfaces before detailed analysis. • By varying the cut-off for contact predictions, AlphaBridge can help distinguish between reliable and unreliable predictions, providing insights into physiological relevance. It was particularly useful for evaluating interactions in DNA mismatch repair proteins and RNA binding proteins. • The AlphaBridge webserver (alpha-bridge.eu) offers an interactive platform where users can upload AlphaFold3 prediction files, visualize the predicted 3D structures, and analyze contact interfaces through an integrated web viewer. • AlphaBridge enhances accessibility for both expert and non-expert users by combining multiple layers of information—contact links, prediction confidence, and visual representations—into one interactive diagram, simplifying the evaluation of complex predictions. @TassosPerrakis @rborza_ 💻Code: github.com/PDB-REDO/Alpha… 📜Paper: biorxiv.org/content/10.110…

(ACS Anal Chem) [ASAP] Is Native Mass Spectrometry in Ammonium Acetate Really Native? Protein Stability Differences in Biochemically Relevant Salt Solutions dlvr.it/TFm6bt (RSS) #MassSpecRSS #ACSAChem

@J_my_sci I'm not sure about Canyon's prizing and service in the US, but i ride Canyon for MTB and Gravel for more than 15 years and can highly recommend their bikes. Best price-performance ratio imo. The big/old brands from the US have pretty frames but are overprized 😉

Awesome! Great progress in synthetic biology & biocomputing. Genetically engineered bacteria can do complex math. nature.com/articles/d4415…

Sören, Giulio & I wrote a short review on the use of machine learning methods to study disordered proteins, with a focus on linking sequences to ensembles (by simulation or generative models; or for design), biophysical properties and biological functions doi.org/10.48550/arXiv…

Phosphorylation can regulate protein function via diverse mechanisms, including the regulation of protein conformations. In our new preprint @m_correa_m compared structures of the same proteins and protein familes in phospho and non phosphorylated forms biorxiv.org/content/10.110…

Meet me up at poster P-I-0053 to the phosphoproteomic changes in mechanical stressed skeletal muscle cells #hupo2024

Role of AAA-ATPase Cdc48p in Peroxisomal Quality Control biorxiv.org/cgi/content/sh… #biorxiv_molbio

Key numbers in biology. 1/2

»Um wen es sich bei diesen „Gollums“ vorrangig handelt, dürfte klar sein: Etablierte Wissenschaftlerinnen und Wissenschaftler, die mit ihren Ergebnissen zu einem bestimmten Forschungsthema bereits Karriere gemacht haben – und jetzt argwöhnisch darüber wachen ...«

📚 New Review by Klaus Pfanner and Nils Wiedemann Biogenesis of mitochondrial β-barrel membrane proteins 🔓buff.ly/3XM15hT #Mitochondria #MembraneProteins #MitoMonday