Sri Devan Appasamy
@sri-appasamy.bsky.social
Bioinformatician at @pdbeurope.bsky.social | Working with macromolecular complexes and RNA. Exploring AI, tech, and the intersection of biology and computing.
ORCID profile: https://orcid.org/0000-0001-6609-3535
ORCID profile: https://orcid.org/0000-0001-6609-3535
Reposted by Sri Devan Appasamy
Our study of time processing in bumblebees 🐝 covered by @cnn.com here edition.cnn.com/2025/11/12/s... . Our summary is here youtu.be/hsGxU65OMQk and the original paper royalsocietypublishing.org/doi/full/10.... @royalsocietypublishing.org
Scientists now know that bees can process time, a first in insects | CNN
Bumblebees can process the duration of flashes of light and use the information to decide where to look for food, a new study has found.
edition.cnn.com
November 22, 2025 at 1:04 PM
Our study of time processing in bumblebees 🐝 covered by @cnn.com here edition.cnn.com/2025/11/12/s... . Our summary is here youtu.be/hsGxU65OMQk and the original paper royalsocietypublishing.org/doi/full/10.... @royalsocietypublishing.org
🚀 Introducing PDBe-KB Complexes — a new PDBe-KB resource for exploring macromolecular complexes across the PDB.
🔗 Explore (SARS-CoV-2 spike, PDB 9CXE): ebi.ac.uk/pdbe/pdbe-kb...
📄 Read the preprint: ssrn.com/abstract=568...
#PDBeKB #MacromolecularComplexes #StructuralBiology
🔗 Explore (SARS-CoV-2 spike, PDB 9CXE): ebi.ac.uk/pdbe/pdbe-kb...
📄 Read the preprint: ssrn.com/abstract=568...
#PDBeKB #MacromolecularComplexes #StructuralBiology
November 14, 2025 at 11:26 AM
Check out the revamped PDBe entry pages!
Making structural biology data accessible to everyone — from specialists to first-time explorers.
✨ Discover the new interactive, personalised & mobile-ready PDBe Entry Pages.
📖 Read more: www.ebi.ac.uk/about/news/u...
🔍 Try it: www.ebi.ac.uk/pdbe/entry/p...
✨ Discover the new interactive, personalised & mobile-ready PDBe Entry Pages.
📖 Read more: www.ebi.ac.uk/about/news/u...
🔍 Try it: www.ebi.ac.uk/pdbe/entry/p...
New PDBe entry pages: Interactive, personalised, and mobile-ready
Explore molecular structures with new interactive 3D viewers and AI annotations
www.ebi.ac.uk
September 19, 2025 at 10:01 AM
Check out the revamped PDBe entry pages!
Reposted by Sri Devan Appasamy
In 2019, we published a clustering & nomenclature of beta turns in proteins & found 18 unique types. The code was in python2. I've just rewritten it in python3, because it might still be useful to people.
The paper & code:
journals.plos.org/ploscompbiol...
github.com/DunbrackLab/...
The paper & code:
journals.plos.org/ploscompbiol...
github.com/DunbrackLab/...
September 5, 2025 at 9:48 AM
In 2019, we published a clustering & nomenclature of beta turns in proteins & found 18 unique types. The code was in python2. I've just rewritten it in python3, because it might still be useful to people.
The paper & code:
journals.plos.org/ploscompbiol...
github.com/DunbrackLab/...
The paper & code:
journals.plos.org/ploscompbiol...
github.com/DunbrackLab/...
We’ve been working on this for the past few years. Give it a try and let us know what we can improve!
🚀 PDBe-KB Complexes (beta) is now live!
Same macromolecular complex. Different experimental conditions. All assemblies in one place.
🔍 Try the beta now: wwwdev.ebi.ac.uk/pdbe/pdbe-kb...
#PDBeKB #Complexes #Bioinformatics #StructuralBiology #Science
Same macromolecular complex. Different experimental conditions. All assemblies in one place.
🔍 Try the beta now: wwwdev.ebi.ac.uk/pdbe/pdbe-kb...
#PDBeKB #Complexes #Bioinformatics #StructuralBiology #Science
September 4, 2025 at 8:26 PM
We’ve been working on this for the past few years. Give it a try and let us know what we can improve!
Reposted by Sri Devan Appasamy
Click on a residue in the sequence viewer or 3D Mol* viewer and watch everything sync! 🎯 Just like magic ✨ — all while zooming in on the structure in real-time.
Try yourself: wwwdev.ebi.ac.uk/pdbe/entry/p...
#PDBeBeta #Molstar #Bioinformatics #ResidueLevelInsights #ARISE #IUCr
Try yourself: wwwdev.ebi.ac.uk/pdbe/entry/p...
#PDBeBeta #Molstar #Bioinformatics #ResidueLevelInsights #ARISE #IUCr
August 13, 2025 at 1:05 PM
Click on a residue in the sequence viewer or 3D Mol* viewer and watch everything sync! 🎯 Just like magic ✨ — all while zooming in on the structure in real-time.
Try yourself: wwwdev.ebi.ac.uk/pdbe/entry/p...
#PDBeBeta #Molstar #Bioinformatics #ResidueLevelInsights #ARISE #IUCr
Try yourself: wwwdev.ebi.ac.uk/pdbe/entry/p...
#PDBeBeta #Molstar #Bioinformatics #ResidueLevelInsights #ARISE #IUCr
Reposted by Sri Devan Appasamy
🧬 🔨 Residue-level insights powered by AI. Explore insight for specific amino acids from primary literature #TextMining
🔍 Check out the ⭐ Text Annotations (AI) ⭐ tab on the new #PDBeBeta pages!
🔗 wwwdev.ebi.ac.uk/pdbe/entry/p...
#AIinBiology #Biology #Science #ARISE #IUCr
🔍 Check out the ⭐ Text Annotations (AI) ⭐ tab on the new #PDBeBeta pages!
🔗 wwwdev.ebi.ac.uk/pdbe/entry/p...
#AIinBiology #Biology #Science #ARISE #IUCr
August 12, 2025 at 4:41 PM
🧬 🔨 Residue-level insights powered by AI. Explore insight for specific amino acids from primary literature #TextMining
🔍 Check out the ⭐ Text Annotations (AI) ⭐ tab on the new #PDBeBeta pages!
🔗 wwwdev.ebi.ac.uk/pdbe/entry/p...
#AIinBiology #Biology #Science #ARISE #IUCr
🔍 Check out the ⭐ Text Annotations (AI) ⭐ tab on the new #PDBeBeta pages!
🔗 wwwdev.ebi.ac.uk/pdbe/entry/p...
#AIinBiology #Biology #Science #ARISE #IUCr
💊 What if we could design drugs for RNA, not just proteins?
lncRNAs like MALAT1, NEAT1, HOTAIR, and GAS5 have structured domains containing loops and bulges that drive function — and can be targeted to treat disease.
Link to paper: tinyurl.com/2vfafxnn
#RNA #lncRNA #DrugDiscovery
lncRNAs like MALAT1, NEAT1, HOTAIR, and GAS5 have structured domains containing loops and bulges that drive function — and can be targeted to treat disease.
Link to paper: tinyurl.com/2vfafxnn
#RNA #lncRNA #DrugDiscovery
August 12, 2025 at 3:58 AM
💊 What if we could design drugs for RNA, not just proteins?
lncRNAs like MALAT1, NEAT1, HOTAIR, and GAS5 have structured domains containing loops and bulges that drive function — and can be targeted to treat disease.
Link to paper: tinyurl.com/2vfafxnn
#RNA #lncRNA #DrugDiscovery
lncRNAs like MALAT1, NEAT1, HOTAIR, and GAS5 have structured domains containing loops and bulges that drive function — and can be targeted to treat disease.
Link to paper: tinyurl.com/2vfafxnn
#RNA #lncRNA #DrugDiscovery
Check out the redesigned AlphaFold Protein Structure Database!
shorturl.at/cuh1u
Try a protein
➡️ alphafold.ebi.ac.uk/entry/Q5VSL9
shorturl.at/cuh1u
Try a protein
➡️ alphafold.ebi.ac.uk/entry/Q5VSL9
New AlphaFold Database entry pages
The AlphaFold Protein Structure Database (AFDB) has redesigned its entry pages to make exploring predicted protein structures faster, clearer, and more intuitive. This update delivers a streamlined ex...
www.ebi.ac.uk
August 8, 2025 at 6:30 PM
Check out the redesigned AlphaFold Protein Structure Database!
shorturl.at/cuh1u
Try a protein
➡️ alphafold.ebi.ac.uk/entry/Q5VSL9
shorturl.at/cuh1u
Try a protein
➡️ alphafold.ebi.ac.uk/entry/Q5VSL9
Reposted by Sri Devan Appasamy
Nice containerization of AlphaFold, Boltz, and Chai, and calculation of metrics (including our ipSAE score for protein-protein interactions). www.biorxiv.org/content/10.1...
August 8, 2025 at 6:11 PM
Nice containerization of AlphaFold, Boltz, and Chai, and calculation of metrics (including our ipSAE score for protein-protein interactions). www.biorxiv.org/content/10.1...
Reposted by Sri Devan Appasamy
Multiple human enhancer RNAs contain long translated open reading frames https://www.biorxiv.org/content/10.1101/2025.04.18.649583v1
April 21, 2025 at 4:17 PM
Multiple human enhancer RNAs contain long translated open reading frames https://www.biorxiv.org/content/10.1101/2025.04.18.649583v1
Reposted by Sri Devan Appasamy
Are you dreaming of RNA? 💭🧬 Then don't miss Alessandro Bonetti and Kevin Weeks at next Thursday's RNA Club! Join us for amazing talks followed by amazing food and drink 🍕🍻 Thank you to our sponsors @rnasociety.bsky.social, Lexogen, IDT and @cambridgebio.bsky.social !
March 13, 2025 at 4:07 PM
Are you dreaming of RNA? 💭🧬 Then don't miss Alessandro Bonetti and Kevin Weeks at next Thursday's RNA Club! Join us for amazing talks followed by amazing food and drink 🍕🍻 Thank you to our sponsors @rnasociety.bsky.social, Lexogen, IDT and @cambridgebio.bsky.social !
Reposted by Sri Devan Appasamy
“We can look to venom, surprisingly, to aid us biomedically," says Dr. Barrett Klein. "For example, bee venom therapy has been used for arthritis, arthralgia, Parkinson’s, ALS, multiple sclerosis, and other conditions.”
How Insects Changed The World—And Human Cultures
In “The Insect Epiphany,” an entomologist explores the history of insects in art, food, engineering, and more.
buff.ly
February 16, 2025 at 3:15 PM
“We can look to venom, surprisingly, to aid us biomedically," says Dr. Barrett Klein. "For example, bee venom therapy has been used for arthritis, arthralgia, Parkinson’s, ALS, multiple sclerosis, and other conditions.”
Reposted by Sri Devan Appasamy
We make a perfect pair!
DNA is composed of a long linear strand of millions of nucleotides, and is most often found paired with a partner strand
DNA is composed of a long linear strand of millions of nucleotides, and is most often found paired with a partner strand
February 14, 2025 at 5:29 PM
We make a perfect pair!
DNA is composed of a long linear strand of millions of nucleotides, and is most often found paired with a partner strand
DNA is composed of a long linear strand of millions of nucleotides, and is most often found paired with a partner strand
Reposted by Sri Devan Appasamy
Find out how @rnacentral.bsky.social are using large language models (LLMs) to automatically generate high-quality literature summaries for noncoding RNAs with their new LitSumm system 👇
bsky.app/profile/rnac...
#RNAsky
bsky.app/profile/rnac...
#RNAsky
February 13, 2025 at 11:24 AM
Find out how @rnacentral.bsky.social are using large language models (LLMs) to automatically generate high-quality literature summaries for noncoding RNAs with their new LitSumm system 👇
bsky.app/profile/rnac...
#RNAsky
bsky.app/profile/rnac...
#RNAsky
Reposted by Sri Devan Appasamy
Reposted by Sri Devan Appasamy
1/12 Excited to share our new paper in DATABASE on LitSumm - our system that uses large language models to automatically generate high-quality literature summaries for non-coding RNAs! 🧬📚
February 7, 2025 at 2:38 PM
1/12 Excited to share our new paper in DATABASE on LitSumm - our system that uses large language models to automatically generate high-quality literature summaries for non-coding RNAs! 🧬📚
Reposted by Sri Devan Appasamy
Happy to share, DesiRNA is now published at Nucleic Acids Research!
doi.org/10.1093/nar/...
DesiRNA is a tool for RNA sequence design (inverse folding) and it is the first to solve all 100 puzzles in the Eterna100 benchmark within 24 h!
#RNA #Design #Research #Bioinformatics #Science #Structure
doi.org/10.1093/nar/...
DesiRNA is a tool for RNA sequence design (inverse folding) and it is the first to solve all 100 puzzles in the Eterna100 benchmark within 24 h!
#RNA #Design #Research #Bioinformatics #Science #Structure
February 7, 2025 at 11:59 AM
Happy to share, DesiRNA is now published at Nucleic Acids Research!
doi.org/10.1093/nar/...
DesiRNA is a tool for RNA sequence design (inverse folding) and it is the first to solve all 100 puzzles in the Eterna100 benchmark within 24 h!
#RNA #Design #Research #Bioinformatics #Science #Structure
doi.org/10.1093/nar/...
DesiRNA is a tool for RNA sequence design (inverse folding) and it is the first to solve all 100 puzzles in the Eterna100 benchmark within 24 h!
#RNA #Design #Research #Bioinformatics #Science #Structure
Reposted by Sri Devan Appasamy
"Dark proteins." Also known as microproteins. There are thousands of them in our cells and we're still struggling to define their function. Succinctly reviewed @nature.com www.nature.com/articles/d41...
‘Dark proteins’ hiding in our cells could hold clues to cancer and other diseases
The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do.
www.nature.com
February 1, 2025 at 4:42 PM
"Dark proteins." Also known as microproteins. There are thousands of them in our cells and we're still struggling to define their function. Succinctly reviewed @nature.com www.nature.com/articles/d41...
Reposted by Sri Devan Appasamy
Learning the language of life with A.I.
@science.org
In today's essay, I review the phenomenal progress in foundation models of DNA, RNA, proteins, ligands, cells, their interactions, the Virtual Lab, and the aspiration for the Virtual Cell
www.science.org/doi/10.1126/...
@science.org
In today's essay, I review the phenomenal progress in foundation models of DNA, RNA, proteins, ligands, cells, their interactions, the Virtual Lab, and the aspiration for the Virtual Cell
www.science.org/doi/10.1126/...
Learning the language of life with AI
In 2021, a year before ChatGPT took the world by storm amid the excitement about generative artificial intelligence (AI), AlphaFold 2 cracked the 50-year-old protein-folding problem, predicting three-...
www.science.org
January 30, 2025 at 7:40 PM
Learning the language of life with A.I.
@science.org
In today's essay, I review the phenomenal progress in foundation models of DNA, RNA, proteins, ligands, cells, their interactions, the Virtual Lab, and the aspiration for the Virtual Cell
www.science.org/doi/10.1126/...
@science.org
In today's essay, I review the phenomenal progress in foundation models of DNA, RNA, proteins, ligands, cells, their interactions, the Virtual Lab, and the aspiration for the Virtual Cell
www.science.org/doi/10.1126/...
Reposted by Sri Devan Appasamy
Reposted by Sri Devan Appasamy
The wwPDB has been featured this week by the Global Biodata Coalition! The wwPDB is a large freely-accessible repository of experimentally determined 3D structures of biological macromolecules.
⬇️Read more⬇️
www.linkedin.com/feed/update/...
⬇️Read more⬇️
www.linkedin.com/feed/update/...
January 27, 2025 at 1:21 PM
The wwPDB has been featured this week by the Global Biodata Coalition! The wwPDB is a large freely-accessible repository of experimentally determined 3D structures of biological macromolecules.
⬇️Read more⬇️
www.linkedin.com/feed/update/...
⬇️Read more⬇️
www.linkedin.com/feed/update/...
Reposted by Sri Devan Appasamy
364 new entries in #PDBrelease (http://PDBe.org/latest)! Here's the cryo-EM derived structure of the human GABAA receptor of β2–α1–β3–α1–γ2 assembly (http://PDBe.org/9cxa). GABAA receptors mediate inhibitory signalling in the brain and are targets of important drugs.
@Nature
@Nature
January 23, 2025 at 9:44 AM
364 new entries in #PDBrelease (http://PDBe.org/latest)! Here's the cryo-EM derived structure of the human GABAA receptor of β2–α1–β3–α1–γ2 assembly (http://PDBe.org/9cxa). GABAA receptors mediate inhibitory signalling in the brain and are targets of important drugs.
@Nature
@Nature
Reposted by Sri Devan Appasamy
Exploring the gap between what LLMs really know vs what people think they know
www.nature.com/articles/s42...
www.nature.com/articles/s42...
What large language models know and what people think they know - Nature Machine Intelligence
Understanding how people perceive and interpret uncertainty from large language models (LLMs) is crucial, as users often overestimate LLM accuracy, especially with default explanations. Steyvers et al...
www.nature.com
January 21, 2025 at 4:08 PM
Exploring the gap between what LLMs really know vs what people think they know
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Cryo-EM can resolve high-resolution structures of small (~200 nt) protein-free ncRNAs using a scaffold-based approach. This breakthrough opens new possibilities for studying RNA structures and advancing RNA-targeted drug discovery
Link: lnkd.in/deQ_s4Tg
Link: lnkd.in/deQ_s4Tg
January 21, 2025 at 6:26 PM
Cryo-EM can resolve high-resolution structures of small (~200 nt) protein-free ncRNAs using a scaffold-based approach. This breakthrough opens new possibilities for studying RNA structures and advancing RNA-targeted drug discovery
Link: lnkd.in/deQ_s4Tg
Link: lnkd.in/deQ_s4Tg