Tom Dongmin Kim
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tomdongmin.bsky.social
Tom Dongmin Kim
@tomdongmin.bsky.social
170 followers 720 following 2 posts
Postdoc @Cardonalab, protein engineering, directed evolution, photosystem II, photosynthesis, HTS, genomics, structural bioinformatics, CRISPR, machine learning
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Reposted by Tom Dongmin Kim
tanaicardona.bsky.social
Our paper on testing #Alphafold predictions and structural phylogenetics of a #photosystem subunit is now published in @pplplantarum.bsky.social. Work by @tomdongmin.bsky.social, with JW Murray & D Pretorius at Imperial. onlinelibrary.wiley.com/doi/full/10.... @qmulse.bsky.social @qmul.ac.uk 🌳
Exploring the Structural Diversity and Evolution of the D1 Subunit of Photosystem II Using AlphaFold and Foldtree
Although our knowledge of photosystem II has expanded to include time-resolved atomic details, the diversity of experimental structures of the enzyme remains limited. Recent advances in protein struc...
onlinelibrary.wiley.com
May 28, 2025 at 5:32 PM
Reposted by Tom Dongmin Kim
spanjikar.bsky.social
Peptide Bonds Unveiled: Enhancing Protein Structure Understanding

Explore the complete study here:
doi.org/10.1107/S205...

#StructuralBiology #AlphaFold #Biochemistry #MolecularBiology #LifeSciences #ComputationalBiology
peptide bonds, Enol, Protonated carbonyl oxygen
April 5, 2025 at 12:21 PM
Reposted by Tom Dongmin Kim
microbesinfo.bsky.social
Evolutionary timeline of #bacteria constructed assisted by machine learning ...

| #microbes | #MachineLearning | #evolution | #photosynthesis | By @keithcowing.bsky.social via @astrobiology.bsky.social
Machine Learning Helps Construct An Evolutionary Timeline Of Bacteria - Astrobiology
University of Queensland scientists have helped to construct a detailed timeline for bacterial evolutio
astrobiology.com
April 6, 2025 at 9:00 PM
Reposted by Tom Dongmin Kim
lovenature.bsky.social
Archaea go multicellular under pressure | Science www.science.org/doi/10.1126/...
Archaea go multicellular under pressure
A microbe from the Dead Sea switches to a tissue-like form when compressed
www.science.org
April 6, 2025 at 5:50 AM
Reposted by Tom Dongmin Kim
acritschristoph.bsky.social
A database of structures for ecologically relevant microbial traits - Looks cool - here's the github: github.com/timghaly/Eco...
April 3, 2025 at 3:24 AM
Reposted by Tom Dongmin Kim
elife.bsky.social
Enhancing the Cre-loxP system: Two new genetic tools – roxCre and loxCre – can improve the performance of the Cre-loxP system for making genetic modifications in vivo.
elifesciences.org/reviewed-pre...
April 3, 2025 at 3:21 AM
Reposted by Tom Dongmin Kim
lindorfflarsen.bsky.social
Supervised training using data generated by multiplexed assays of variant effects is potentially very powerful, but is made difficult by assay- and protein-specific effects

Here @tkschulze.bsky.social devised a strategy to take this into account while training models
www.biorxiv.org/content/10.1...
Figure illustrating the framework for supervised learning across VAMP-seq datasets.
April 3, 2025 at 3:03 AM
Reposted by Tom Dongmin Kim
delalamo.xyz
Dedicated protein stability prediction methods, such as ThermoMPNN and RASP, universally perform worse than advertised when tested on rebalanced datasets with natural AA distributions & substitution rates www.biorxiv.org/content/10.1...
: A scatterplot of the Pearson Correlation Coefficient (PCC) of the full S4038 dataset (black), and the balanced subsets (red) and random subsets (blue). For many of the benchmarked tools (x-axis), there is a clear separation between the balanced subsets and the random subsets, where the balanced subsets tend to have lower PCCs towards the experimental data.
April 3, 2025 at 5:20 AM
Reposted by Tom Dongmin Kim
biorxiv-synthbio.bsky.social
Chemically Synthesized Ultra-long DNA as Building Blocks to Accelerate Complex Gene Construction in Synthetic Biology https://www.biorxiv.org/content/10.1101/2025.04.02.646740v1
April 3, 2025 at 3:04 AM
Reposted by Tom Dongmin Kim
structbioinfo.bsky.social
Read this paper from Twitter/X and it was a good read. academic.oup.com/bioinformati...
A BLAST from the past: revisiting blastp’s E-value
AbstractMotivation. The Basic Local Alignment Search Tool, BLAST, is an indispensable tool for genomic research. BLAST has established itself as the canoni
academic.oup.com
March 29, 2025 at 1:14 AM
Reposted by Tom Dongmin Kim
cyanotrans.bsky.social
Enhancing the production of chlorophyll f in the cyanobacterium Synechocystis sp. PCC 6803 onlinelibrary.wiley.com/doi/full/10....
Enhancing the production of chlorophyll f in the cyanobacterium Synechocystis sp. PCC 6803
One potential approach to improve the productivity of cyanobacteria and microalgae is to enhance photosynthetic efficiency by introducing far-red absorbing pigment molecules (such as chlorophylls f a...
onlinelibrary.wiley.com
March 28, 2025 at 11:19 AM
Reposted by Tom Dongmin Kim
stephenturner.us
Review: Transcriptomics in the era of long-read sequencing www.nature.com/articles/s41... (read free: rdcu.be/efBjP) 🧬🖥️🧪
March 29, 2025 at 8:57 AM
Reposted by Tom Dongmin Kim
oborkowski.bsky.social
NAND Hybrid Riboswitch Design by Deep Batch Bayesian Optimization
doi.org/10.1101/2025...
March 29, 2025 at 9:54 AM
Reposted by Tom Dongmin Kim
openfold.io
Read more about this new data sharing agreement that allows #OpenFold's lead AI scientist, Mohammed AlQuraishi, to use proprietary data to train state-of-the-art generative AI models. This is uniquely possible because OpenFold is fully #openSource!
AbbVie, J&J to add proprietary data to AI protein model in bid to accelerate drug discovery
Imagine standing on a vast, dark plain. Without light, you cannot see dips and rolls in the grass or make out hills and valleys. Even if there’s a city
www.statnews.com
March 28, 2025 at 4:06 PM
Reposted by Tom Dongmin Kim
martinsteinegger.bsky.social
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Google Colab
colab.research.google.com
March 29, 2025 at 9:50 AM
Reposted by Tom Dongmin Kim
cjjackson.bsky.social
biorxiv.org/content/10.1... Here’s a paper that was many years in the making. The idea that the climate can affect the thermodynamic mechanism of binding due to the temperature dependence of the entropy term is interesting- we see gradual shift in binding mode along evo trajectory…
March 26, 2025 at 5:13 AM
Reposted by Tom Dongmin Kim
iscb.bsky.social
Today’s COSI spotlight is on HiTSeq: High Throughput Sequencing Algorithms and Applications!

HiTSeq focuses on the latest computational advances for analyzing high-throughput sequencing data.
March 18, 2025 at 9:01 AM
Reposted by Tom Dongmin Kim
dialecticbio.bsky.social
Deep learning for proteins tutorial: github.com/Graylab/DL4P...
GitHub - Graylab/DL4Proteins-notebooks: Colab Notebooks covering deep learning tools for biomolecular structure prediction and design
Colab Notebooks covering deep learning tools for biomolecular structure prediction and design - Graylab/DL4Proteins-notebooks
github.com
December 28, 2024 at 3:15 AM
Reposted by Tom Dongmin Kim
ebi.embl.org
🚀 #AlphaFold Database update

AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.

www.ebi.ac.uk/about/news/u...

@pdbeurope.bsky.social
March 3, 2025 at 4:33 PM
Reposted by Tom Dongmin Kim
lorendw.bsky.social
My second ever Bluesky post:

Another part of the work of my wonderful graduate student Kavita Matange (post doc at CSHL) has come out here (open access).

pubs.acs.org/doi/full/10....
Biological Polymers: Evolution, Function, and Significance
ConspectusA holistic description of biopolymers and their evolutionary origins will contribute to our understanding of biochemistry, biology, the origins of life, and signatures of life outside our pl...
pubs.acs.org
March 8, 2025 at 5:05 AM
Reposted by Tom Dongmin Kim
tanaicardona.bsky.social
Our work applying #AlphaFold prediction and structural phylogenetics to the D1 subunit of #photosystem II is now on BioRxiv! This project was spearheaded by @tomdongmin.bsky.social in my lab, in collab with D. Pretorius and J. W. Murray. Check it out: www.biorxiv.org/content/10.1... #photosynthesis
Exploring the structural diversity and evolution of the D1 subunit of photosystem II using AlphaFold and Foldtree
While our knowledge of photosystem II has expanded to time-resolved atomic details, the diversity of experimental structures of the enzyme remains limited. Recent advances in protein structure predict...
www.biorxiv.org
March 7, 2025 at 10:13 AM
tomdongmin.bsky.social
It’s on! The first step to bring the evolution of photosystem into 3D with structure prediction.
biorxiv-bioinfo.bsky.social bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Mar 7
Exploring the structural diversity and evolution of the D1 subunit of photosystem II using AlphaFold and Foldtree https://www.biorxiv.org/content/10.1101/2025.03.06.641835v1
March 7, 2025 at 9:22 AM
Reposted by Tom Dongmin Kim
drmikebooth.bsky.social
🚨 Preprint alert 🚨 We have developed an entirely new mechanism of action for ASO gene knockdown -> lysosomal trafficking!

Works with non-DNA ASOs (unlike RNase H mech) and higher activity than corresponding gapmers!

#chemsky 🧪 @uclchemistry.bsky.social sky.social
chemrxiv.org/engage/chemr...
Engineering antisense oligonucleotides for targeted mRNA degradation through lysosomal trafficking
Antisense oligonucleotides (ASOs) can modulate gene expression at the mRNA level, providing the ability to tackle conventionally undruggable targets and usher in an era of personalized medicine. A key...
chemrxiv.org
March 7, 2025 at 8:51 AM
Reposted by Tom Dongmin Kim
oborkowski.bsky.social
Programming Nutrient Detection with Modular Regulators for Dynamic Control of Microbial Biosynthesis
pubs.acs.org/doi/abs/10.1...
Programming Nutrient Detection with Modular Regulators for Dynamic Control of Microbial Biosynthesis
Dynamic control of biosynthetic pathways improves the bioproduction efficiency. One common approach is to use genetic sensors that control pathway expression in response to a nutrient molecule in the ...
pubs.acs.org
March 7, 2025 at 8:15 AM