🤖 Can AI help us predict and prevent off-target effects in PROTAC drug design?

🔗 Predicting PROTAC off-target effects via warhead involvement levels in drug–target interactions using graph attention neural networks. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.028

📚 CSBJ: https://www.csbj.org/

#DrugDevelopment #StructuralBiology #ChemicalBiology #PROTAC #DrugDiscovery #Cheminformatics #Bioinformatics #PrecisionMedicine #TargetedProteinDegradation

🧬 Can entropy help us decode how hormone receptors make real-time decisions?

🔗 Temporal complexity of LVV-hemorphin-7 allosterism at the angiotensin II type 1 receptor assessed using entropy-based approaches. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.024

📚 CSBJ: https://www.csbj.org/

#StructuralBiology #Biophysics #GPCR #Entropy #MolecularPharmacology #AllostericModulation #DrugDiscovery #MolecularDynamics

New Title Alert: Pom- a tool for scaling data analyses in cellular cryoET using comprehensive segmentation.

Learn more here: https://github.com/bionanopatterning/Pom

#SBGrid #SBGridSoftware #StructuralBiology

SBGrid's eLife paper received a citation in October from Jean-Philippe Julien from The Hospital for Sick Children Research Institute in Immunity:

Cryo-EM structure of endogenous Pfs230:Pfs48/45 complex with six antibodies reveals mechanisms of malaria transmission-blocking activity.

Read more here: https://www.cell.com/immunity/fulltext/S1074-7613(25)00425-X?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=579&lea=37746&ctr=0&par=1&trk=a0NNv0000015qv3MAA

#SBGrid #StructuralBiology

New Title Alert: OpenEye Academic Package- tools to help design potent and selective bioactive molecules.

Learn more here: https://www.eyesopen.com/

#SBGrid #SBGridSoftware #StructuralBiology

Late and still at work
PDB deposition
Bug in the portal

#haiku #StructuralBiology

New Title Alert: nvMolKit- is a CUDA-backed Python library for accelerating common RDKit molecular operations through batch-oriented GPU processing.

Learn more here: https://nvidia-digital-bio.github.io/nvMolKit/#

#SBGrid #SBGridSoftware #StructuralBiology

Postdoctoral fellow wanted in virology
NYU Grossman School of Medicine

See the full job description on jobRxiv: https://jobrxiv.org/job/nyu-grossman-school-of-medicine-27778-postdoctoral-fellow-wanted-in-virology/

#biochemistry #immunology #structuralbiology #virology #ScienceJobs #hiring #research
https://jobrxiv.org/job/nyu-grossman-school-of-medicine-27778-postdoctoral-fellow-wanted-in-virology/?fsp_sid=5702

✨ Is it time to rethink allosteric site prediction using internal protein nanoenvironments?

🔗 Protein allosteric site identification using machine learning and per amino acid residue reported internal protein nanoenvironment descriptors. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.10.036

📚 CSBJ: https://www.csbj.org/

#DrugDiscovery #ComputationalBiology #StructuralBiology #ProteinEngineering #Biophysics #Cheminformatics

💊 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

New Title Alert: Icecream- a self-supervised framework for cryo-ET reconstruction that integrates equivariance principles from modern imaging theory into a deep-learning architecture.

Learn more here: https://github.com/swing-research/icecream

#SBGrid #SBGridSoftware #StructuralBiology

🧬 Ever wondered how the genome actually looks when it folds inside the nucleus — and how fast we can simulate it?

🔗 Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.09.025

📚 CSBJ: https://www.csbj.org/

#ChromatinModeling #3DGenome #ComputationalBiology #Genomics #MolecularModeling #GenomeArchitecture #ChromatinStructure #HiC #ATACSeq #Biophysics #StructuralBiology

🧬 Can salt levels change how cell-penetrating peptides behave at membranes?

🔗 Molecular dynamics simulations unveil the aggregation patterns and salting out of polyarginines at zwitterionic POPC bilayers in solutions of various ionic strengths. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.004

📚 CSBJ: https://www.csbj.org/

#MolecularDynamics #PeptideAggregation #MembraneProtein #Biophysics #StructuralBiology #ProteinFolding #MembraneBiology

Join us November 18th to hear from Hui Wang, postdoc in the Hong Zhou lab at University of California, Los Angeles, on TomoNet: Automatic Particle Picking of Flexible Lattice-Like Structures for CryoET.

Register here: https://sbgrid.org/webinars/

#SBGrid #StructuralBiology #Webinars

🧬 How do changes in a non-catalytic residue collapse an entire enzyme’s function?

🔗 Conformational plasticity links structural instability of NAA10F128I and NAA10F128L mutants to their catalytic deregulation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.014

📚 CSBJ: https://www.csbj.org/

#Biophysics #Enzymology #StructuralBiology #Mutations #ProteinFolding

💧 Is your MD simulation lying to you because of the water model you picked?

🔗 Impact of water models on the structure and dynamics of enzyme tunnels. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.10.051

📚 CSBJ: https://www.csbj.org/

#ComputationalBiology #MolecularDynamics #Enzymology #StructuralBiology #ProteinEngineering #Biophysics #WaterModels #EnzymeTunnels #MolecularSimulation #ProteinDynamics

🧩 What if the diverse functions of a single protein all trace back to one structural superfamily?

🔗 Evolutionary and structural bioinformatics identifies GPR89 as a conserved member of the LIMR protein superfamily. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.003

📚 CSBJ: https://www.csbj.org/

#StructuralBiology #ComputationalBiology #MolecularEvolution #ProteinScience #Genomics #Proteomics #AlphaFold #MembraneProteins #Genetics #Bioinformatics

New Title Alert: SimpleFold- is the first flow-matching based protein folding model that uses only general purpose transformer layers, without relying on expensive modules like triangle attention or pair representation biases.

Learn more here: https://github.com/apple/ml-simplefold

#SBGrid #SBGridSoftware #StructuralBiology

New Title Alert: CTFMeasure- a software for estimating CTF parameters of cryo-ET tilt series. It features tilt-series-based joint estimation and Thon ring rescaling technique to retrieve power spectrums with higher SNR and more clear Thon rings, leading to higher estimation accuracy.

Learn more here: https://thuem.net/software/ctfmeasure/overview.html

#SBGrid #SBGridSoftware #StructuralBiology