Tom Dongmin Kim

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...

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 🌳

peptide bonds, Enol, Protonated carbonyl oxygen

Peptide Bonds Unveiled: Enhancing Protein Structure Understanding

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

#StructuralBiology #AlphaFold #Biochemistry #MolecularBiology #LifeSciences #ComputationalBiology

Machine Learning Helps Construct An Evolutionary Timeline Of Bacteria - Astrobiology University of Queensland scientists have helped to construct a detailed timeline for bacterial evolutio

Evolutionary timeline of #bacteria constructed assisted by machine learning ...

| #microbes | #MachineLearning | #evolution | #photosynthesis | By @keithcowing.bsky.social via @astrobiology.bsky.social

Siemens Agrees to Buy Dotmatics for $5.1 Billion, Expanding AI Portfolio to Life Sciences The deal extends Siemens’s artificial-intelligence-powered product-lifecycle-management portfolio and increases the company’s total addressable market in industrial software by $11 billion.

Dotmatics, the company that owns GraphPad Prism, Geneious and SnapGene was just acquired by Siemens for $5.1B. With plans to create AI-based software www.wsj.com/business/dea...

Archaea go multicellular under pressure A microbe from the Dead Sea switches to a tissue-like form when compressed

Archaea go multicellular under pressure | Science www.science.org/doi/10.1126/...

A database of structures for ecologically relevant microbial traits - Looks cool - here's the github: github.com/timghaly/Eco...

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...

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...

: 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.

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...

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

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

Read this paper from Twitter/X and it was a good read. academic.oup.com/bioinformati...

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...

Enhancing the production of chlorophyll f in the cyanobacterium Synechocystis sp. PCC 6803 onlinelibrary.wiley.com/doi/full/10....

Review: Transcriptomics in the era of long-read sequencing www.nature.com/articles/s41... (read free: rdcu.be/efBjP) 🧬🖥️🧪

NAND Hybrid Riboswitch Design by Deep Batch Bayesian Optimization
doi.org/10.1101/2025...

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

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!

Google Colab

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...

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…

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.

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

Deep learning for proteins tutorial: github.com/Graylab/DL4P...

🚀 #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

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...

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....

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...

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

It’s on! The first step to bring the evolution of photosystem into 3D with structure prediction.

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...

🚨 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...

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 ...

Programming Nutrient Detection with Modular Regulators for Dynamic Control of Microbial Biosynthesis
pubs.acs.org/doi/abs/10.1...

Nice work!

FEBS Press The transcription and mRNA structures of the alkane biosynthesis genes ado/aar were analysed in the representative cyanobacteria PCC 6803 and SK1-2-1, which produce C17H36 and C15H32, respectively. P...

Alkane biosynthesis gene expression and its increased production in recombinant cyanobacteria febs.onlinelibrary.wiley.com/doi/full/10....

Product release and substrate entry of aldehyde deformylating oxygenase revealed by molecular dynamics simulations Cyanobacteria can produce alkanes equivalent to diesel fuels through a two-step enzymatic process involving acyl-(acyl carrier protein) reductase (AAR …

Product release and substrate entry of aldehyde deformylating oxygenase revealed by molecular dynamics simulations doi.org/10.2142/biop...

Nipah virus G protein with 16813 ligands (mostly waters) mapped from similar structures.

ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...

Evidencing nickel biosorption capacity of cyanobacteria Chroococcidiopsis sp.: potential metallo-protective agents - BMC Chemistry The increasing prevalence of toxic elements such as nickel (Ni) in the environment poses a significant threat to human health due to its carcinogenic effect. The study investigates the Ni biosorption ...

Evidencing nickel biosorption capacity of cyanobacteria Chroococcidiopsis sp.: potential metallo-protective agents bmcchem.biomedcentral.com/articles/10....