#molecularsimulation — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #molecularsimulation, aggregated by home.social.
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Looking forward to comparisons, experiences, and pointers to similar tools. #ComputationalChemistry #Enzymology #QMMM #MachineLearning #MolecularSimulation #MLforScience #ReactionMechanisms #DrugDiscovery #HPC #ChemRxiv 🧵 12/12
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💧 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
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💧 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
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⚛️ 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
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⚛️ 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
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🧬 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
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🧬 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
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🧬 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
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🧬 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
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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 🧪
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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 🧪
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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? 🌍
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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? 🌍
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📝 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
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Congrats to Tim Marshall for successfully defending his #PhD Thesis!
Tim's work focused on using MSMs as a platform for evaluating force fields and examining whether simulations can quantitatively predict how mutations affect folding stability, toward the prospect of simulation-based virtual screening for protein design. Several manuscripts describing this work are still in preparation, so stay tuned for preprints.
#compchem #chemistry #molecularsimulation #biophysics #Temple
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Congrats to Tim Marshall for successfully defending his #PhD Thesis!
Tim's work focused on using MSMs as a platform for evaluating force fields and examining whether simulations can quantitatively predict how mutations affect folding stability, toward the prospect of simulation-based virtual screening for protein design. Several manuscripts describing this work are still in preparation, so stay tuned for preprints.
#compchem #chemistry #molecularsimulation #biophysics #Temple
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Happy to see another command I worked on merged in the LAMMPS code.
Langevin barostat is now available to use, thanks to the dev team which is of very wise help.
Waiting for users feedback, if any. 😊
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Unlocking the secrets of materials & designing new ones starts w/ #molecularsimulation. Our Research Software Engineer (#RSE) Aron Jansen describes how #machinelearning is revolutionizing this field in a 3-part blog series. Part 1 explores the fundamental theory of quantum mechanics behind it all!
https://medium.com/@aronpjansen/e8624a82f680?source=friends_link&sk=8c9902b39588261826ab77e3e24f8766
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Unlocking the secrets of materials & designing new ones starts w/ #molecularsimulation. Our Research Software Engineer (#RSE) Aron Jansen describes how #machinelearning is revolutionizing this field in a 3-part blog series. Part 1 explores the fundamental theory of quantum mechanics behind it all!
https://medium.com/@aronpjansen/e8624a82f680?source=friends_link&sk=8c9902b39588261826ab77e3e24f8766
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I’m an Associate Professor of #chemistry at #TempleUniv. My #compchem lab uses #molecularsimulation and #statmech to study #protein dynamics.
Researcher with Folding@home, Interested in leveraging distributed simulations and #ML for #drugdiscovery, especially for foldable #cyclicpeptides, designed miniproteins, and #peptoids; #bayesian inference fan.
I look forward to learning about all the #science people are doing, and being part of a non-algorithmic ad-free space!