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#moleculardynamics — Public Fediverse posts

Live and recent posts from across the Fediverse tagged #moleculardynamics, aggregated by home.social.

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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. ⚛️ 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: doi.org/10.34133/csbj.0024

    📚 CSBJ Quantum Biology and Biophotonics: spj.science.org/journal/csbj/q

    #QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences

  7. ⚛️ 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: doi.org/10.34133/csbj.0024

    📚 CSBJ Quantum Biology and Biophotonics: spj.science.org/journal/csbj/q

    #QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences

  8. ⚛️ 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: doi.org/10.34133/csbj.0024

    📚 CSBJ Quantum Biology and Biophotonics: spj.science.org/journal/csbj/q

    #QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences

  9. ⚛️ 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: doi.org/10.34133/csbj.0024

    📚 CSBJ Quantum Biology and Biophotonics: spj.science.org/journal/csbj/q

    #QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences

  10. ⚛️ 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: doi.org/10.34133/csbj.0024

    📚 CSBJ Quantum Biology and Biophotonics: spj.science.org/journal/csbj/q

    #QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences

  11. 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.

  12. 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.

  13. 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.

  14. 🚀 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: doi.org/10.1016/j.csbj.2025.11

    📚 CSBJ: csbj.org/

    #DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery

  15. 🚀 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: doi.org/10.1016/j.csbj.2025.11

    📚 CSBJ: csbj.org/

    #DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery

  16. 🚀 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: doi.org/10.1016/j.csbj.2025.11

    📚 CSBJ: csbj.org/

    #DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery

  17. 🚀 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: doi.org/10.1016/j.csbj.2025.11

    📚 CSBJ: csbj.org/

    #DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery

  18. 🚀 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: doi.org/10.1016/j.csbj.2025.11

    📚 CSBJ: csbj.org/

    #DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery

  19. 🔬 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: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

    #ComputationalBiology #MolecularDynamics #StructuralBiology #CancerResearch #AML #DrugDiscovery #PrecisionMedicine #KinaseResearch #Bioinformatics

  20. 🔬 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: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

    #ComputationalBiology #MolecularDynamics #StructuralBiology #CancerResearch #AML #DrugDiscovery #PrecisionMedicine #KinaseResearch #Bioinformatics

  21. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

    #COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology

  22. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

    #COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology

  23. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

    #COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology

  24. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

    #COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology

  25. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

    #COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 🧬 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: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

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

  32. 🧬 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: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. Nuestro pequeño cluster para cálculos de dinámica molecular en el CURE. Configurar este cluster fue una gran experiencia que amplió notablemente mis conocimientos previos de sysadmin con Undernet. Le saco poco cartel #cluster #moleculardynamics #cure #udelar #diy #physics #debian #slurm #openmpi

  39. Nuestro pequeño cluster para cálculos de dinámica molecular en el CURE. Configurar este cluster fue una gran experiencia que amplió notablemente mis conocimientos previos de sysadmin con Undernet. Le saco poco cartel #cluster #moleculardynamics #cure #udelar #diy #physics #debian #slurm #openmpi

  40. Nuestro pequeño cluster para cálculos de dinámica molecular en el CURE. Configurar este cluster fue una gran experiencia que amplió notablemente mis conocimientos previos de sysadmin con Undernet. Le saco poco cartel #cluster #moleculardynamics #cure #udelar #diy #physics #debian #slurm #openmpi

  41. Nuestro pequeño cluster para cálculos de dinámica molecular en el CURE. Configurar este cluster fue una gran experiencia que amplió notablemente mis conocimientos previos de sysadmin con Undernet. Le saco poco cartel #cluster #moleculardynamics #cure #udelar #diy #physics #debian #slurm #openmpi

  42. Nuestro pequeño cluster para cálculos de dinámica molecular en el CURE. Configurar este cluster fue una gran experiencia que amplió notablemente mis conocimientos previos de sysadmin con Undernet. Le saco poco cartel #cluster #moleculardynamics #cure #udelar #diy #physics #debian #slurm #openmpi

  43. 💊 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: doi.org/10.1016/j.csbj.2024.10

    📚 CSBJ: csbj.org/

    #GPCR #StructuralBiology #MolecularDynamics #NMR #Pharmacology #ProteinStructure #DrugDiscovery #ComputationalBiology #CellSignaling