#moleculardynamics — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #moleculardynamics, aggregated by home.social.
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Brute force simulations.
"These proteins should form a pore through which RNA can pass."
Me: Manually places the RNA in the middle of the proteins on a membrane and hopes for a miracle (or a pore).
#compchem #simulation #moleculardynamics #proteinStructure #rna #protein #academicchatter #chemistry #pymol
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Brute force simulations.
"These proteins should form a pore through which RNA can pass."
Me: Manually places the RNA in the middle of the proteins on a membrane and hopes for a miracle (or a pore).
#compchem #simulation #moleculardynamics #proteinStructure #rna #protein #academicchatter #chemistry #pymol
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Brute force simulations.
"These proteins should form a pore through which RNA can pass."
Me: Manually places the RNA in the middle of the proteins on a membrane and hopes for a miracle (or a pore).
#compchem #simulation #moleculardynamics #proteinStructure #rna #protein #academicchatter #chemistry #pymol
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Brute force simulations.
"These proteins should form a pore through which RNA can pass."
Me: Manually places the RNA in the middle of the proteins on a membrane and hopes for a miracle (or a pore).
#compchem #simulation #moleculardynamics #proteinStructure #rna #protein #academicchatter #chemistry #pymol
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Brute force simulations.
"These proteins should form a pore through which RNA can pass."
Me: Manually places the RNA in the middle of the proteins on a membrane and hopes for a miracle (or a pore).
#compchem #simulation #moleculardynamics #proteinStructure #rna #protein #academicchatter #chemistry #pymol
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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Funded PhD - multiscale electrochemical modeling
University College DublinSee the full job description on jobRxiv: https://jobrxiv.org/job/university-college-dublin-27778-funded-phd-multiscale-electrochemical-modeling/
#battery #computationalfluiddynamics #electrochemistry #moleculardynamics #quantumchemistry #ScienceJobs #hiring #research
https://jobrxiv.org/job/university-college-dublin-27778-funded-phd-multiscale-electrochemical-modeling/?fsp_sid=10273 -
Sometimes I imagine an LLM model trained on the #LAMMPS forum and mailing-list basically answering most #moleculardynamics related questions with:
* You should (re)read the manual.
* There are not enough information to conclude about your results.
* What do you expect in the first place?
* Garbage in, garbage out.
* As Axel Kohlmeyer said here...
* Talk to your advisor.
* This is expected and documented behavior.In think that in this case it would actually be helpful.
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🚀 What if we could precisely target the CAPON–nNOS axis — a pathway long considered undruggable?
🔗 Targeting CAPON to modulate the CAPON–NOS Axis: a computational approach. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.001
📚 CSBJ: https://www.csbj.org/
#DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery
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🚀 What if we could precisely target the CAPON–nNOS axis — a pathway long considered undruggable?
🔗 Targeting CAPON to modulate the CAPON–NOS Axis: a computational approach. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.001
📚 CSBJ: https://www.csbj.org/
#DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery
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🚀 What if we could precisely target the CAPON–nNOS axis — a pathway long considered undruggable?
🔗 Targeting CAPON to modulate the CAPON–NOS Axis: a computational approach. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.001
📚 CSBJ: https://www.csbj.org/
#DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery
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🚀 What if we could precisely target the CAPON–nNOS axis — a pathway long considered undruggable?
🔗 Targeting CAPON to modulate the CAPON–NOS Axis: a computational approach. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.001
📚 CSBJ: https://www.csbj.org/
#DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery
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🚀 What if we could precisely target the CAPON–nNOS axis — a pathway long considered undruggable?
🔗 Targeting CAPON to modulate the CAPON–NOS Axis: a computational approach. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.001
📚 CSBJ: https://www.csbj.org/
#DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery
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🔬 Can structural shifts at the atomic level decide treatment outcomes in AML?
🔗 Understanding the characteristic behaviour of the wild-type and mutant structure of FLT3 protein by computational methods. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.023
📚 CSBJ: https://www.csbj.org/
#ComputationalBiology #MolecularDynamics #StructuralBiology #CancerResearch #AML #DrugDiscovery #PrecisionMedicine #KinaseResearch #Bioinformatics
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🔬 Can structural shifts at the atomic level decide treatment outcomes in AML?
🔗 Understanding the characteristic behaviour of the wild-type and mutant structure of FLT3 protein by computational methods. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.023
📚 CSBJ: https://www.csbj.org/
#ComputationalBiology #MolecularDynamics #StructuralBiology #CancerResearch #AML #DrugDiscovery #PrecisionMedicine #KinaseResearch #Bioinformatics
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🧬 How did changes at the atomic scale reshape viral infectivity?
🔗 Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.07.034
📚 CSBJ: https://www.csbj.org/
#COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology
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🧬 How did changes at the atomic scale reshape viral infectivity?
🔗 Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.07.034
📚 CSBJ: https://www.csbj.org/
#COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology
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🧬 How did changes at the atomic scale reshape viral infectivity?
🔗 Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.07.034
📚 CSBJ: https://www.csbj.org/
#COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology
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🧬 How did changes at the atomic scale reshape viral infectivity?
🔗 Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.07.034
📚 CSBJ: https://www.csbj.org/
#COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology
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🧬 How did changes at the atomic scale reshape viral infectivity?
🔗 Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.07.034
📚 CSBJ: https://www.csbj.org/
#COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology
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Sat my butt down, drank too much :neofox_cofe: coffee, and wrote an introductory blog post exploring the amazing world of molecular dynamics. Bewhold! Check it out and do let me know what you think! :neofox_uwu: ❤️ Thank yoooou!
https://bugwhisperer.dev/blog/exploring-the-world-of-molecular-dynamics/
gemini://capsule.bugwhisperer.dev/posts/exploring-the-world-of-molecular-dynamics.gmi
#molecularDynamics #biophysics #blogging #scienceRules #computationalBiology -
🧬 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
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🧬 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
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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 -
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 -
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 -
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 -
💊 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
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💊 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
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🧬 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
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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 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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🧬 Can molecular simulations transform the future of long-acting diabetes treatments?
🔗 In silico investigations of albumin-GLP-1 receptor agonist complexes for diabetes drug delivery applications. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.007
📚 CSBJ: https://www.csbj.org/
#MolecularDynamics #DiabetesResearch #Biotherapeutics #GLP1 #Albumin #DrugDelivery #Biomaterials #ComputationalBiology #ProteinEngineering
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🧬 Can molecular simulations transform the future of long-acting diabetes treatments?
🔗 In silico investigations of albumin-GLP-1 receptor agonist complexes for diabetes drug delivery applications. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.007
📚 CSBJ: https://www.csbj.org/
#MolecularDynamics #DiabetesResearch #Biotherapeutics #GLP1 #Albumin #DrugDelivery #Biomaterials #ComputationalBiology #ProteinEngineering
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🧫 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
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🧫 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
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🧫 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
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🧫 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
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🔬 Could a tiny imbalance in ATP binding be the key to drug resistance in cancer?
🔗 Nucleotide asymmetry and flexible linker dynamics modulate drug efflux cycle of P-glycoprotein, A computational study. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.064
📚 CSBJ: https://www.csbj.org/
#DrugResistance #MolecularDynamics #StructuralBiology #MembraneProteins #CancerResearch #Pharmacology #DrugDiscovery #ChemotherapyResistance #ProteinDynamics #Pgp #ABCB1 #Biophysics
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⚡️ How does the Hv1 proton channel conduct protons faster than diffusion should allow?
🔗 Fluctuating hydrogen-bond network of the Hv1 ion channel. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.021
📚 CSBJ: https://www.csbj.org/
#Biophysics #ProtonChannel #MolecularDynamics #StructuralBiology #HydrogenBonding #IonChannels #ProtonTransport #Hv1
