#molecularmodeling — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #molecularmodeling, aggregated by home.social.
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New Algorithmic Scrutiny Targets Molecular Migrations in Drug Development
University of Oregon's new AI tool helps drug makers test new molecules faster and cheaper. It predicts how drugs will work before lab tests.
#DrugDiscovery, #AIinPharma, #UniversityOfOregon, #MolecularModeling, #HealthcareTech
https://newsletter.tf/oregon-university-ai-speeds-up-drug-making/
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This new AI tool from the University of Oregon can help create new medicines much faster than before. It uses computers to predict how molecules will behave.
#DrugDiscovery, #AIinPharma, #UniversityOfOregon, #MolecularModeling, #HealthcareTech
https://newsletter.tf/oregon-university-ai-speeds-up-drug-making/ -
🧩 Could RNA and proteins share the same “shape language” for binding drugs?
🔗 Eigenvalue Ratios Reveal Shared Binding Pocket Shapes in RNA and Protein Structures. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0022
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#DrugDiscovery #StructuralBiology #ComputationalBiology #RNAResearch #ProteinScience #Bioinformatics #MolecularModeling #Genomics #Proteomics #Cheminformatics #LigandBinding
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🧩 Could RNA and proteins share the same “shape language” for binding drugs?
🔗 Eigenvalue Ratios Reveal Shared Binding Pocket Shapes in RNA and Protein Structures. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0022
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#DrugDiscovery #StructuralBiology #ComputationalBiology #RNAResearch #ProteinScience #Bioinformatics #MolecularModeling #Genomics #Proteomics #Cheminformatics #LigandBinding
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I've got a Masters proposal presentation tomorrow. Why am I so anxious all the time? I chose this topic, I know it enough to propose it and I love it. Why can't I just chill? :blobcatscared: #physicalchemistry #molecularmodeling #kmc #ComputationalChemistry
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New paper in JCIM:
GPU-accelerated ab initio ESP calculations in QUICK + a reweighted RESP (rwRESP) scheme for robust, grid density–independent charge fitting.Dense molecular grids eliminate orientation dependence in ESP charge derivation. rwRESP removes grid sensitivity and is now integrated into AmberTools.
Open-source and reproducible.
Paper: https://doi.org/10.1021/acs.jcim.5c03200
QUICK: https://github.com/merzlab/QUICK -
New paper in JCIM:
GPU-accelerated ab initio ESP calculations in QUICK + a reweighted RESP (rwRESP) scheme for robust, grid density–independent charge fitting.Dense molecular grids eliminate orientation dependence in ESP charge derivation. rwRESP removes grid sensitivity and is now integrated into AmberTools.
Open-source and reproducible.
Paper: https://doi.org/10.1021/acs.jcim.5c03200
QUICK: https://github.com/merzlab/QUICK -
New paper in JCIM:
GPU-accelerated ab initio ESP calculations in QUICK + a reweighted RESP (rwRESP) scheme for robust, grid density–independent charge fitting.Dense molecular grids eliminate orientation dependence in ESP charge derivation. rwRESP removes grid sensitivity and is now integrated into AmberTools.
Open-source and reproducible.
Paper: https://doi.org/10.1021/acs.jcim.5c03200
QUICK: https://github.com/merzlab/QUICK -
New paper in JCIM:
GPU-accelerated ab initio ESP calculations in QUICK + a reweighted RESP (rwRESP) scheme for robust, grid density–independent charge fitting.Dense molecular grids eliminate orientation dependence in ESP charge derivation. rwRESP removes grid sensitivity and is now integrated into AmberTools.
Open-source and reproducible.
Paper: https://doi.org/10.1021/acs.jcim.5c03200
QUICK: https://github.com/merzlab/QUICK -
New paper in JCIM:
GPU-accelerated ab initio ESP calculations in QUICK + a reweighted RESP (rwRESP) scheme for robust, grid density–independent charge fitting.Dense molecular grids eliminate orientation dependence in ESP charge derivation. rwRESP removes grid sensitivity and is now integrated into AmberTools.
Open-source and reproducible.
Paper: https://doi.org/10.1021/acs.jcim.5c03200
QUICK: https://github.com/merzlab/QUICK -
✨ What secret molecular partnership helps mycobacteria stay alive when conditions turn deadly?
🔗 Structural modeling and biochemical characterization of MSMEG_0748, a MoxR ATPase from Mycobacterium smegmatis. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.010
📚 CSBJ: https://www.csbj.org/
#Mycobacterium #MoxR #ATPase #AlphaFold #StructuralBiology #Biophysics #Microbiology #MolecularModeling
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✨ What secret molecular partnership helps mycobacteria stay alive when conditions turn deadly?
🔗 Structural modeling and biochemical characterization of MSMEG_0748, a MoxR ATPase from Mycobacterium smegmatis. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.010
📚 CSBJ: https://www.csbj.org/
#Mycobacterium #MoxR #ATPase #AlphaFold #StructuralBiology #Biophysics #Microbiology #MolecularModeling
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✨ What secret molecular partnership helps mycobacteria stay alive when conditions turn deadly?
🔗 Structural modeling and biochemical characterization of MSMEG_0748, a MoxR ATPase from Mycobacterium smegmatis. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.010
📚 CSBJ: https://www.csbj.org/
#Mycobacterium #MoxR #ATPase #AlphaFold #StructuralBiology #Biophysics #Microbiology #MolecularModeling
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✨ What secret molecular partnership helps mycobacteria stay alive when conditions turn deadly?
🔗 Structural modeling and biochemical characterization of MSMEG_0748, a MoxR ATPase from Mycobacterium smegmatis. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.010
📚 CSBJ: https://www.csbj.org/
#Mycobacterium #MoxR #ATPase #AlphaFold #StructuralBiology #Biophysics #Microbiology #MolecularModeling
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4/n Vor allem das leichte #Headset und die mühelose Fähigkeit zu #Kommunikation und #Interaktion mehrerer Benutzer untereinander am selben Gerät fällt im Vergleich zu anderen Geräten positiv auf.
#MINT #STEM #Bioinformatik #CompChem #MolecularModeling #AR #VR #MR #Lehre #Schule #Rechenkraft #education #school #HessenHub
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4/n Vor allem das leichte #Headset und die mühelose Fähigkeit zu #Kommunikation und #Interaktion mehrerer Benutzer untereinander am selben Gerät fällt im Vergleich zu anderen Geräten positiv auf.
#MINT #STEM #Bioinformatik #CompChem #MolecularModeling #AR #VR #MR #Lehre #Schule #Rechenkraft #education #school #HessenHub
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4/n Vor allem das leichte #Headset und die mühelose Fähigkeit zu #Kommunikation und #Interaktion mehrerer Benutzer untereinander am selben Gerät fällt im Vergleich zu anderen Geräten positiv auf.
#MINT #STEM #Bioinformatik #CompChem #MolecularModeling #AR #VR #MR #Lehre #Schule #Rechenkraft #education #school #HessenHub
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4/n Vor allem das leichte #Headset und die mühelose Fähigkeit zu #Kommunikation und #Interaktion mehrerer Benutzer untereinander am selben Gerät fällt im Vergleich zu anderen Geräten positiv auf.
#MINT #STEM #Bioinformatik #CompChem #MolecularModeling #AR #VR #MR #Lehre #Schule #Rechenkraft #education #school #HessenHub
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4/n Vor allem das leichte #Headset und die mühelose Fähigkeit zu #Kommunikation und #Interaktion mehrerer Benutzer untereinander am selben Gerät fällt im Vergleich zu anderen Geräten positiv auf.
#MINT #STEM #Bioinformatik #CompChem #MolecularModeling #AR #VR #MR #Lehre #Schule #Rechenkraft #education #school #HessenHub
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🧬 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
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🧬 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
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1/n Gestern habe ich am Standort #Gießen der "Labs for Innovative Teaching — Network for Impactful Digital International Teaching Skills (#NIDIT)" das Rechenkraft.net #AugmentedReality Visualisierungssystem für molekulare Objekte (a.k.a. #HoloDeck) über mehr als drei Stunden zum Ausprobieren bereit gestellt.
#MINT #STEM #CitizenScience #Schule #AR #VR #Gamification #Game2Learn #TiltFive #Rechenkraft #CompChem #Bioinformatik #MolecularModeling #Proteine #Nukleinsäuren #DNA #RNA
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1/n Gestern habe ich am Standort #Gießen der "Labs for Innovative Teaching — Network for Impactful Digital International Teaching Skills (#NIDIT)" das Rechenkraft.net #AugmentedReality Visualisierungssystem für molekulare Objekte (a.k.a. #HoloDeck) über mehr als drei Stunden zum Ausprobieren bereit gestellt.
#MINT #STEM #CitizenScience #Schule #AR #VR #Gamification #Game2Learn #TiltFive #Rechenkraft #CompChem #Bioinformatik #MolecularModeling #Proteine #Nukleinsäuren #DNA #RNA
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Am vergangenen Donnerstag (30.10.2025) wurde der zweite #HoloDeck-Kurs zur Visualisierung molekularer Objekte in #AugmentedReality an der #JLU #Gießen präsentiert.
#MINT #STEM #CitizenScience #Universität #Schule #AR #VR #MR #Gamification #Game2Learn #TiltFive #Rechenkraft #CompChem #Bioinformatik #MolecularModeling
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Am vergangenen Donnerstag (30.10.2025) wurde der zweite #HoloDeck-Kurs zur Visualisierung molekularer Objekte in #AugmentedReality an der #JLU #Gießen präsentiert.
#MINT #STEM #CitizenScience #Universität #Schule #AR #VR #MR #Gamification #Game2Learn #TiltFive #Rechenkraft #CompChem #Bioinformatik #MolecularModeling
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Places are still available on our three-day online course in molecular modelling and computational chemistry on LRZ HPC Systems. 👩🔬
🗓️ 18.11.2025 – 20.11.2025
🔗 https://tiny.badw.de/rVV04UThis online course introduces the fundamental principles and key concepts of #molecularmodeling on LRZ HPC systems. Participants will be introduced to several molecular dynamics software packages and learn how to use them effectively.
Register now!
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Just chatted about the future of molecular modeling and realized we lean too much on automation. AI is powerful, but those “aha” moments from years of intuition still drive breakthroughs. Human‑in‑the‑loop lets us spot patterns, tackle edge cases, and guide data toward creative solutions. How do you balance automation with expertise in your work? 🤔
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Just chatted about the future of molecular modeling and realized we lean too much on automation. AI is powerful, but those “aha” moments from years of intuition still drive breakthroughs. Human‑in‑the‑loop lets us spot patterns, tackle edge cases, and guide data toward creative solutions. How do you balance automation with expertise in your work? 🤔
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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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Posting this months after GGMM 2025 on purpose: the takeaways still hold. Strong mix of structural bioinformatics, AI, integrative/multi‑scale modeling, and visualization; great PhD/postdoc–senior interplay. MolPlay feedback aged well and is shaping follow‑ups. Grateful for the community—see you in two years.
#GGMM2025 #MolecularModeling #ComputationalBiology #ScientificCommunity
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🧬 Can we bridge the gap between AlphaFold’s static structures and real molecular motion?
🔗 Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.047
📚 CSBJ: https://www.csbj.org/
#Biophysics #ProteinDynamics #AlphaFold #CABSflex #StructuralBiology #ComputationalBiology #MolecularModeling #Bioinformatics #MolecularDynamics #ProteinFlexibility
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🧬 Can we bridge the gap between AlphaFold’s static structures and real molecular motion?
🔗 Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.047
📚 CSBJ: https://www.csbj.org/
#Biophysics #ProteinDynamics #AlphaFold #CABSflex #StructuralBiology #ComputationalBiology #MolecularModeling #Bioinformatics #MolecularDynamics #ProteinFlexibility
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💡 AI can predict protein structures — but can it predict how they behave?
🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.015
📚 CSBJ: https://www.csbj.org/
#AlphaFold3 #ProteinDesign #MolecularModeling #ComputationalBiology #StructuralBiology #Thermodynamics #ProteinProteinInteractions #Bioinformatics
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💡 AI can predict protein structures — but can it predict how they behave?
🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.015
📚 CSBJ: https://www.csbj.org/
#AlphaFold3 #ProteinDesign #MolecularModeling #ComputationalBiology #StructuralBiology #Thermodynamics #ProteinProteinInteractions #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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🧩 The future of drug discovery may depend on how well we understand PROTAC-driven protein partnerships.
🔗 Mapping the energy landscape of PROTAC-mediated protein-protein interactions. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2023.02.049
📚 CSBJ: https://www.csbj.org/
#StructuralBiology #PROTAC #DrugDiscovery #ComputationalBiology #ProteinEngineering #ProteinDegradation #Biopharma #MedicinalChemistry #TargetedTherapies #AIinBiotech #MolecularModeling
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🧩 The future of drug discovery may depend on how well we understand PROTAC-driven protein partnerships.
🔗 Mapping the energy landscape of PROTAC-mediated protein-protein interactions. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2023.02.049
📚 CSBJ: https://www.csbj.org/
#StructuralBiology #PROTAC #DrugDiscovery #ComputationalBiology #ProteinEngineering #ProteinDegradation #Biopharma #MedicinalChemistry #TargetedTherapies #AIinBiotech #MolecularModeling
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I am shamefully copying this post from Linkedin but if you happen to know any candidate, do not hesitate to reach:
It's on. To my #ComputationalChemistry network, I am calling on you. 🙇
The PM2E team in the CIMAP laboratory (www.cimap.ensicaen.fr) is looking for a #PhD hashtag#candidate. The goal of the project is to understand key parameters in #semiconductor defects stability and physics (both vacancies and color centers, see for example: https://doi.org/10.1016/j.nimb.2022.12.025) through the use of
#DFT and #MolecularModeling. The end goals of the project is concerned with application for #QuantumComputing through the making of stable #qubit. Collaboration and communication with experimentalists will be part of the project.If you're interested in #MolecularDynamics, #MonteCarlo simulations, or DFT and quantum calculations, we are waiting for you. We are using codes such as #Lammps and #QuantumEspresso. We are looking for a candidate finishing or already having a master degree (or equivalent diploma) with training in #physics/ #MaterialsScience / #TheoreticalChemistry. Any experience in programming using #Python, #C and the #Linux environment would be considered a plus.
The position is located in Alençon (Orne) between Caen and Le Mans. Founding is assured for relevant candidates.
Link to the offer (in french, you can ask for an english version): https://www.abg.asso.fr/en/candidatOffres/show/id_offre/127985/job/simulation-atomistique-de-defauts-crees-par-irradiation-dans-les-semiconducteurs
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I am shamefully copying this post from Linkedin but if you happen to know any candidate, do not hesitate to reach:
It's on. To my #ComputationalChemistry network, I am calling on you. 🙇
The PM2E team in the CIMAP laboratory (www.cimap.ensicaen.fr) is looking for a #PhD hashtag#candidate. The goal of the project is to understand key parameters in #semiconductor defects stability and physics (both vacancies and color centers, see for example: https://doi.org/10.1016/j.nimb.2022.12.025) through the use of
#DFT and #MolecularModeling. The end goals of the project is concerned with application for #QuantumComputing through the making of stable #qubit. Collaboration and communication with experimentalists will be part of the project.If you're interested in #MolecularDynamics, #MonteCarlo simulations, or DFT and quantum calculations, we are waiting for you. We are using codes such as #Lammps and #QuantumEspresso. We are looking for a candidate finishing or already having a master degree (or equivalent diploma) with training in #physics/ #MaterialsScience / #TheoreticalChemistry. Any experience in programming using #Python, #C and the #Linux environment would be considered a plus.
The position is located in Alençon (Orne) between Caen and Le Mans. Founding is assured for relevant candidates.
Link to the offer (in french, you can ask for an english version): https://www.abg.asso.fr/en/candidatOffres/show/id_offre/127985/job/simulation-atomistique-de-defauts-crees-par-irradiation-dans-les-semiconducteurs
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#Compchem #esr #chimie #ThinFilm #MolecularDynamic #MolecularModeling #Science #Recherche
On me fait part d'une offre de poste d'enseignant-chercheur au Gremi d'Orléans pour modéliser les interactions #plasma surfaces pour les dépôts de couches minces. Plus d'infos ici: https://unicloud.unicaen.fr/index.php/s/HSpScY7td9Ce8Tm
Contactez [email protected]
Le repouet sympathique est apprécié.