The Dracarys Award: Classiq Quantum AI
For withstanding The Quantum Dragon’s relentless assault, I do hereby proclaim Classiq Quantum AI the fourth recipient of The Dracarys Award.
https://bsiegelwax.substack.com/p/the-dracarys-award-classiq-quantum
#QuantumComputing #MolecularSimulation #ComputationalChemistry #ClassiqPlatform #QuantumAI
💧 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
⚛️ Is the secret to circular rare earth recovery hidden in molecular motion?
🔗 Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.02.005
📚 CSBJ: https://www.csbj.org/
#RareEarths #Lanmodulin #ComputationalBiology #Sustainability #CircularEconomy #RareEarthElements #MolecularDynamics #ProteinEngineering #MolecularModeling #MolecularSimulation
🧬 Could a single residue swap turn a life-saving antibody into a “dead mutant”?
🔗 Replacement of a single residue in an antibody abolishes cognate antigen binding, as predicted by theoretical methods. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.018
📚 CSBJ: https://www.csbj.org/
#AntibodyEngineering #StructuralBiology #ComputationalBiology #ProteinModeling #Biophysics #Diagnostics #MolecularDynamics #MolecularSimulation #InfraredSpectroscopy #FTIR
🧬 How does a foodborne toxin punch holes in our cells?
🔗 C. perfringens enterotoxin-claudin pore complex: Models for structure, mechanism of pore assembly and cation permeability. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.048
📚 CSBJ: https://www.csbj.org/
#StructuralBiology #ComputationalBiology #ToxinResearch #AlphaFold2 #MolecularDynamics #Claudin #CPE #FoodSafety #MolecularSimulation #ProteinComplex #Bioinformatics
🧬 When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.003
📚 CSBJ: https://www.csbj.org/
#RNA #StructuralBiology #CASP15 #ComputationalBiology #Bioinformatics #MolecularSimulation #MolecularDynamics #Biophysics #MolecularModeling
BioSpring presents an elastic network framework for hands-on, real‑time probing of macromolecular mechanics—augmenting springs with electrostatics, implicit membranes, and density fitting. Nice demos: protein flexibility, protein–DNA docking, membrane insertion. Curious how folks integrate such interactive steps before heavy MD?
#molecularsimulation #structuralbiology #interactive #opensource 🧪
This work presents BioSpring, a lightweight simulation framework that lets researchers explore macromolecules interactively, in real time. It augments classic elastic network models with practical force terms—van der Waals, Coulomb, implicit membranes, precomputed electrostatic fields, density fitting, and solvent accessibility—so users can probe flexibility, allostery, docking, and membrane interactions without heavy compute. The engine links to visualization and optional haptics, enabling intuitive push‑pull manipulation while remaining within biophysically sensible energy ranges. Demonstrations include protein conformational changes, elastic protein–DNA docking guided by fields, and membrane protein insertion using implicit bilayers, with turnkey setups via MolPlay and open‑source code at https://biospring.mol3d.tech ↗.
Computational chemistry thrives when teams are diverse—in culture, training, and perspective. It shapes the questions we ask and the tools we build, from quantum methods to classical MD. Let’s keep widening the circle and share practical ways to make labs more inclusive. Anyone piloting programs that work? 🌍
📝 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
Horacio Pérez-Sánchez
Brian Siegelwax
CSBJ
Marc Baaden