#proteinstructure — Public Fediverse posts

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

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

⚛️ Can spherical voxelization improve how AI interprets protein chemistry and interactions?

🔗 SpheronizaTor: Spherical Voxelization for Interpretable Protein Microenvironment Modeling. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0076

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#StructuralBiology #Bioinformatics #ComputationalBiology #ProteinStructure #ArtificialIntelligence #ProteinEngineering #ProteinModeling

⚛️ Can spherical voxelization improve how AI interprets protein chemistry and interactions?

🔗 SpheronizaTor: Spherical Voxelization for Interpretable Protein Microenvironment Modeling. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0076

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#StructuralBiology #Bioinformatics #ComputationalBiology #ProteinStructure #ArtificialIntelligence #ProteinEngineering #ProteinModeling

Pipeline release! nf-core/proteinfold v2.0.0 - Montseny Brook Newt!
Protein 3D structure prediction pipeline
Please see the changelog: https://github.com/nf-core/proteinfold/releases/tag/2.0.0

#alphafold2 #colabfold #esmfold #proteinfoldprediction #proteinfolding #proteinsequences #proteinstructure #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/proteinfold v2.0.0 - Montseny Brook Newt!
Protein 3D structure prediction pipeline
Please see the changelog: https://github.com/nf-core/proteinfold/releases/tag/2.0.0

#alphafold2 #colabfold #esmfold #proteinfoldprediction #proteinfolding #proteinsequences #proteinstructure #nfcore #openscience #nextflow #bioinformatics

Structural Changes in Blood Proteins Could Enable Early Detection of Alzheimer’s Disease

📰 Original title: A surprising blood protein pattern may reveal Alzheimer’s

🤖 IA: It's not clickbait ✅
👥 Usuarios: It's not clickbait ✅

View full AI summary: https://killbait.com/en/structural-changes-in-blood-proteins-could-enable-early-detection-of-alzheimers-disease/?redirpost=49afce0e-391d-42a6-bd7a-829c3952b1e9

#health #alzheimers #bloodtest #proteinstructure

AI Transforms Scientific Discovery: How AlphaFold and AI Co-Scientist Are Reshaping Research

https://techlife.blog/posts/ai-transforms-scientific-discovery-alphafold-ai-co-scientist/

#AlphaFold #Google #DeepMind #ScientificDiscovery #ProteinStructure #Gemini #NobelPrize #AIResearch #AlphaEvolve #BioNeMo #AI

AI Transforms Scientific Discovery: How AlphaFold and AI Co-Scientist Are Reshaping Research

https://techlife.blog/posts/ai-transforms-scientific-discovery-alphafold-ai-co-scientist/

#AlphaFold #Google #DeepMind #ScientificDiscovery #ProteinStructure #Gemini #NobelPrize #AIResearch #AlphaEvolve #BioNeMo #AI

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

💊 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

🧫 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

🧫 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

16-Sep-2025
Better understanding of #bitter #taste receptors: An AlphaFold3-based structure study
Researchers use an advanced AI-based prediction model, #AlphaFold 3, to predict the structure of human bitter taste #receptors
https://www.eurekalert.org/news-releases/1098406

#science #humans #physiology #proteinstructure

16-Sep-2025
Better understanding of #bitter #taste receptors: An AlphaFold3-based structure study
Researchers use an advanced AI-based prediction model, #AlphaFold 3, to predict the structure of human bitter taste #receptors
https://www.eurekalert.org/news-releases/1098406

#science #humans #physiology #proteinstructure

🌀 Could a protein that twists into filaments reveal how cells keep themselves in balance?

🔗 Cryo-EM structure of AAA + ATPase thorase reveals novel helical filament formation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.018

📚 CSBJ: https://www.csbj.org/

#StructuralBiology #CryoEM #Thorase #MolecularBiology #mTORC1 #ProteinStructure #Biophysics #AAAplusATPase #SynapticPlasticity #Mitochondria

🌀 Could a protein that twists into filaments reveal how cells keep themselves in balance?

🔗 Cryo-EM structure of AAA + ATPase thorase reveals novel helical filament formation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.018

📚 CSBJ: https://www.csbj.org/

#StructuralBiology #CryoEM #Thorase #MolecularBiology #mTORC1 #ProteinStructure #Biophysics #AAAplusATPase #SynapticPlasticity #Mitochondria

Sometimes while reading scientific articles I feel like they just slammed the keyboard randomly.

#AcademicChatter #proteinStructure

Sometimes while reading scientific articles I feel like they just slammed the keyboard randomly.

#AcademicChatter #proteinStructure

I am excited to introduce our new @EvolLetters paper that has just come out:

https://academic.oup.com/evlett/advance-article/doi/10.1093/evlett/qraf026/8223096

🧵1/7

#temperature #adaptation #enzyme #microbes #ProteinStructure

I am excited to introduce our new @EvolLetters paper that has just come out:

https://academic.oup.com/evlett/advance-article/doi/10.1093/evlett/qraf026/8223096

🧵1/7

#temperature #adaptation #enzyme #microbes #ProteinStructure

🪨 Can sand-like molecules help us map the secrets of protein structure?

🔗 Adsorption of silica oligomers on biomolecules: Structural and dynamical insights for atom probe tomography via classic molecular dynamics simulations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.004

📚 CSBJ: https://www.csbj.org/

#AtomProbeTomography #MolecularDynamics #Biophysics #ProteinStructure #Nanotech #ComputationalBiology #StructuralBiology #Biomaterials #ProteinScience

🪨 Can sand-like molecules help us map the secrets of protein structure?

🔗 Adsorption of silica oligomers on biomolecules: Structural and dynamical insights for atom probe tomography via classic molecular dynamics simulations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.004

📚 CSBJ: https://www.csbj.org/

#AtomProbeTomography #MolecularDynamics #Biophysics #ProteinStructure #Nanotech #ComputationalBiology #StructuralBiology #Biomaterials #ProteinScience

DATE: June 18, 2025 at 07:00AM
SOURCE: BioWorld MedTech

Direct article link at end of text block below.

Alphadesign: #AI creating #proteins from scratch

https://t.co/eXSDSBx0mv

#medtech #designerprotein #proteinstructure

Here are any URLs found in the article text:

https://t.co/eXSDSBx0mv

#medtech

Articles can be found by scrolling down the page at https://www.bioworld.com/topics/85-bioworld-medtech .

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#healthcare #healthtech #healthcaretech #healthtechnology #medgadget #medicine #doctor #hospital #medtech

DATE: June 18, 2025 at 07:00AM
SOURCE: BioWorld MedTech

Direct article link at end of text block below.

Alphadesign: #AI creating #proteins from scratch

https://t.co/eXSDSBx0mv

#medtech #designerprotein #proteinstructure

Here are any URLs found in the article text:

https://t.co/eXSDSBx0mv

#medtech

Articles can be found by scrolling down the page at https://www.bioworld.com/topics/85-bioworld-medtech .

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Private, vetted email list for mental health professionals: https://www.clinicians-exchange.org
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NYU Information for Practice puts out 400-500 good quality health-related research posts per week but its too much for many people, so that bot is limited to just subscribers. You can read it or subscribe at @PsychResearchBot
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Since 1991 The National Psychologist has focused on keeping practicing psychologists current with news, information and items of interest. Check them out for more free articles, resources, and subscription information: https://www.nationalpsychologist.com
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EMAIL DAILY DIGEST OF RSS FEEDS -- SUBSCRIBE:
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#healthcare #healthtech #healthcaretech #healthtechnology #medgadget #medicine #doctor #hospital #medtech

DATE: June 17, 2025 at 05:00PM
SOURCE: BioWorld MedTech

Direct article link at end of text block below.

Alphadesign: #AI creating #proteins from scratch

https://t.co/eXSDSBwswX

#medtech #designerprotein #proteinstructure

Here are any URLs found in the article text:

https://t.co/eXSDSBwswX

#medtech

Articles can be found by scrolling down the page at https://www.bioworld.com/topics/85-bioworld-medtech .

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Private, vetted email list for mental health professionals: https://www.clinicians-exchange.org
.
NYU Information for Practice puts out 400-500 good quality health-related research posts per week but its too much for many people, so that bot is limited to just subscribers. You can read it or subscribe at @PsychResearchBot
.
Since 1991 The National Psychologist has focused on keeping practicing psychologists current with news, information and items of interest. Check them out for more free articles, resources, and subscription information: https://www.nationalpsychologist.com
.
EMAIL DAILY DIGEST OF RSS FEEDS -- SUBSCRIBE:
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#healthcare #healthtech #healthcaretech #healthtechnology #medgadget #medicine #doctor #hospital #medtech

DATE: June 17, 2025 at 05:00PM
SOURCE: BioWorld MedTech

Direct article link at end of text block below.

Alphadesign: #AI creating #proteins from scratch

https://t.co/eXSDSBwswX

#medtech #designerprotein #proteinstructure

Here are any URLs found in the article text:

https://t.co/eXSDSBwswX

#medtech

Articles can be found by scrolling down the page at https://www.bioworld.com/topics/85-bioworld-medtech .

-------------------------------------------------

Private, vetted email list for mental health professionals: https://www.clinicians-exchange.org
.
NYU Information for Practice puts out 400-500 good quality health-related research posts per week but its too much for many people, so that bot is limited to just subscribers. You can read it or subscribe at @PsychResearchBot
.
Since 1991 The National Psychologist has focused on keeping practicing psychologists current with news, information and items of interest. Check them out for more free articles, resources, and subscription information: https://www.nationalpsychologist.com
.
EMAIL DAILY DIGEST OF RSS FEEDS -- SUBSCRIBE:
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#healthcare #healthtech #healthcaretech #healthtechnology #medgadget #medicine #doctor #hospital #medtech

🧩 What happens when we put AlphaFold2’s predictions to the ultimate test—across species and structure types?

🔗 Comprehensive assessment of AlphaFold’s predictions of secondary structure and solvent accessibility at the amino acid-level in eukaryotic, bacterial and archaeal proteins. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.047

📚 CSBJ: https://www.csbj.org/

#AlphaFold #Bioinformatics #StructuralBiology #AlphaFold2 #ProteinStructure #ProteinPrediction #AI

🧬 How do AlphaFold2 and ESMFold stack up when it comes to functional annotation?

🔗 AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.01.008

📚 CSBJ: https://www.csbj.org/

#AlphaFold2 #ESMFold #AIinScience #ProteinStructure #Enzymes #Pfam #UniProt #AlphaFold #HumanProteome #FunctionalAnnotation #AIinBiology #ComputationalBiology #FunctionalGenomics

`Recent research highlights the transition from a pathological to a functional perspective of amyloid fibrils, paving the way for innovative applications in biotechnology and materials science. By leveraging the self-assembly properties and biocompatibility of functional amyloids, advancements in drug delivery, tissue engineering, and nanotechnology are emerging`

https://arxiv.org/abs/2504.15532

#proteinStructure #betaSheet

`Recent research highlights the transition from a pathological to a functional perspective of amyloid fibrils, paving the way for innovative applications in biotechnology and materials science. By leveraging the self-assembly properties and biocompatibility of functional amyloids, advancements in drug delivery, tissue engineering, and nanotechnology are emerging`

https://arxiv.org/abs/2504.15532

#proteinStructure #betaSheet

🧠 Can post-processing and deep learning push protein prediction to near perfection?

🔗 Post-processing enhances protein secondary structure prediction with second order deep learning and embeddings. DOI: https://doi.org/10.1016/j.csbj.2024.12.022

📚 CSBJ: https://www.csbj.org/

#DeepLearning #Proteins #PSSP #ProteinStructure #ProtBERT #CNN #AlphaFold #AI #Proteomics

📝 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

DEADLINE EXTENDED: The new deadline for submission of manuscripts for this special issue is 31 January 2025.

📝 Call for Papers: Special Issue on "AlphaFold in Protein Structure and Function Prediction".

🔗Link to the 'Call for Papers': https://www.csbj.org/call_AlphaFold

📊 Guest Editors:

🌟Lukasz Kurgan, Virginia Commonwealth University, United States of America
🌟Jianyi Yang, Shandong University, China

#AlphaFold #ProteinStructure #ProteinFunction #DrugDesign #TargetPrediction

2024 Nobel in Chemistry for “Designing protein” and “Predicting protein structure”  
One half of the Nobel Prize in Chemistry 2024 has been awarded to David Baker “for computational protein design”............
#AImodel #AlphaFold2 #Aminoacids #DavidBaker #DemisHassabis #JohnJumper #NobelPrizeinChemistry #PROTEIN #Proteindesign #Proteinstructure
SC

https://www.scientificeuropean.co.uk/sciences/chemistry/2024-nobel-in-chemistry-for-designing-protein-and-predicting-protein-structure/

2024 Nobel in Chemistry for “Designing protein” and “Predicting protein structure”  
One half of the Nobel Prize in Chemistry 2024 has been awarded to David Baker “for computational protein design”............
#AImodel #AlphaFold2 #Aminoacids #DavidBaker #DemisHassabis #JohnJumper #NobelPrizeinChemistry #PROTEIN #Proteindesign #Proteinstructure
SC

https://www.scientificeuropean.co.uk/sciences/chemistry/2024-nobel-in-chemistry-for-designing-protein-and-predicting-protein-structure/

Elizabeth Villa's lab delivers big time again with in-cell cryo-electron tomography of the nuclear pore complex:

"The molecular architecture of the nuclear basket" by Singh et al. 2024.
https://www.cell.com/cell/fulltext/S0092-8674(24)00780-3

#CellBiology #CryoEM #ProteinStructure #StructuralBiology

Elizabeth Villa's lab delivers big time again with in-cell cryo-electron tomography of the nuclear pore complex:

"The molecular architecture of the nuclear basket" by Singh et al. 2024.
https://www.cell.com/cell/fulltext/S0092-8674(24)00780-3

#CellBiology #CryoEM #ProteinStructure #StructuralBiology

From the annals of Alphafold surfing, I was looking at some yeast-specific genes in preparation for a talk that will feature what you can learn by studying yeast-specific genes.

Look at this beauty:

ECM33-somehow involved in glucose uptake, extracellular GPI anchored protein.
#AlphaFold #StructuralBiology #ProteinStructure

From the annals of Alphafold surfing, I was looking at some yeast-specific genes in preparation for a talk that will feature what you can learn by studying yeast-specific genes.

Look at this beauty:

ECM33-somehow involved in glucose uptake, extracellular GPI anchored protein.
#AlphaFold #StructuralBiology #ProteinStructure

AlphaFold 3 is out but... https://macinchem.org/2024/05/10/alphafold-3-is-out-but/ #ArtificialIntelligence #proteinstructure
#compchem

AlphaFold 3 is out but... https://macinchem.org/2024/05/10/alphafold-3-is-out-but/ #ArtificialIntelligence #proteinstructure
#compchem

AlphaFold3 is now available and looks like it can handle all molecule interactions!

Webserver: https://golgi.sandbox.google.com/about
Paper: https://www.nature.com/articles/s41586-024-07487-w

#AlphaFold #AlphaFold3 #ProteinStructure

Just Published

Advanced Technologies for Protein Complex Production and Characterization. Volume II.

https://link.springer.com/book/10.1007/978-3-031-52193-5

This edited volume discusses the identification, discovery, characterization, structure determination and modeling of multicomponent macromolecular complexes.

The first volume (https://link.springer.com/book/10.1007/978-3-319-27216-0), targeted methods of recombinant production of protein complexes.

Enjoy!

#ProteinComplexes #Biochemistry #ExpressionSystems #Protein #ProteinStructure #SystemsBiology

Just Published

Advanced Technologies for Protein Complex Production and Characterization. Volume II.

https://link.springer.com/book/10.1007/978-3-031-52193-5

This edited volume discusses the identification, discovery, characterization, structure determination and modeling of multicomponent macromolecular complexes.

The first volume (https://link.springer.com/book/10.1007/978-3-319-27216-0), targeted methods of recombinant production of protein complexes.

Enjoy!

#ProteinComplexes #Biochemistry #ExpressionSystems #Protein #ProteinStructure #SystemsBiology

Antibodies against anything? AI tool adapted to make them - Enlarge

Antibodies are incredibly useful. Lots of recently de... - https://arstechnica.com/?p=2011766 #proteinstructure #computerscience #diffusionmodel #biochemistry #antibody #proteins #science #biology #ai

Antibodies against anything? AI tool adapted to make them - Enlarge

Antibodies are incredibly useful. Lots of recently de... - https://arstechnica.com/?p=2011766 #proteinstructure #computerscience #diffusionmodel #biochemistry #antibody #proteins #science #biology #ai

✨ @SWISS_MODEL has a fresh new logo!

It evokes four globular chains of interacting proteins, as #SWISS-MODEL allows to model protein complexes in 3D. Discover this leading #ProteinStructure homology-modelling platform, one of the 14 leading Open Science bioinformatics resources developed by our teams to serve millions of scientists.

SIB provides support to enhance brand visibility of its resources alongside UX, data protection...

👉 Read more: https://www.sib.swiss/services/open-software-and-databases

#ProteinModeling

✨ @SWISS_MODEL has a fresh new logo!

It evokes four globular chains of interacting proteins, as #SWISS-MODEL allows to model protein complexes in 3D. Discover this leading #ProteinStructure homology-modelling platform, one of the 14 leading Open Science bioinformatics resources developed by our teams to serve millions of scientists.

SIB provides support to enhance brand visibility of its resources alongside UX, data protection...

👉 Read more: https://www.sib.swiss/services/open-software-and-databases

#ProteinModeling

@cmdcolin

I use Alphafold (actually colabfold) and am happy to answer questions, but I'm just a user. There are people with more expertise than me here.

Hashtags might find the right people

#StructurePrediction #alphafold #alphafold2 #colabfold #ProteinStructure #StructuralBiology #ProteinPrediction #protein #bioinformatics

4-JAN-2024
Breakthrough in designing complicated all-α protein structures

https://www.eurekalert.org/news-releases/1030258 #science #proteins #nanoworld #ProteinDesign #ProteinStructure #AlphaHelix

@cjrlab

Chris, would you say that your 100 keV approach to protein structure determination democratises #cryoEM ? That for a lot of purposes there's no need any more for the largely unaffordable Titan Krios?

#ProteinStructure

Just watched a couple of brilliant YouTube videos by biologist Jake Brown

Cells aren’t fancy clockwork machines: https://youtube.com/watch?v=jPhvic-eqbc
(Further reading: https://www.subanima.org/veritasium/)

Mendel wasn’t a Mendelian: https://youtube.com/watch?v=zpIqQ0pGs1E
(Further reading: https://www.subanima.org/mendel/)

(I was going to support Jake via his Patreon page, but unfortunately he’s not accepting new subscribers at the moment)

#CellBiology #genetics #MendelianInheritance #Mendel #ProteinStructure #ProteinFolding #TeachingBiology #SRYgene #CancerGenes #HumanGenomeProject #SystemsBiology #WaddingtonLandscape

"Starting at Go: #Protein structure prediction succumbs to machine learning" (PNAS)

https://www.pnas.org/doi/10.1073/pnas.2311128120

#ProteinStructure #MachineLearning