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Reposted by Tom Dongmin Kim

Tanai Cardona @tanaicardona.bsky.social · May 28

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

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Reposted by Tom Dongmin Kim

Santosh Panjikar @spanjikar.bsky.social · Apr 5

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

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Reposted by Tom Dongmin Kim

Microbes.Info @microbesinfo.bsky.social · Apr 6

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

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Reposted by Tom Dongmin Kim

Vega Shah @dr-alphalyrae.bsky.social · Apr 6

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...

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.

www.wsj.com

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Reposted by Tom Dongmin Kim

藤井　恒 @lovenature.bsky.social · Apr 6

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

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Reposted by Tom Dongmin Kim

Alex Crits-Christoph @acritschristoph.bsky.social · Apr 3

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

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Reposted by Tom Dongmin Kim

eLife @elife.bsky.social · Apr 3

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...

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Reposted by Tom Dongmin Kim

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Apr 3

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.

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Reposted by Tom Dongmin Kim

Diego del Alamo @delalamo.xyz · Apr 3

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.

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Reposted by Tom Dongmin Kim

bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · Apr 3

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

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Reposted by Tom Dongmin Kim

Ragothaman Yennamalli @structbioinfo.bsky.social · Mar 29

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

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Reposted by Tom Dongmin Kim

Cyanotrans @cyanotrans.bsky.social · Mar 28

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

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Reposted by Tom Dongmin Kim

Stephen Turner @stephenturner.us · Mar 29

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

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Reposted by Tom Dongmin Kim

Olivier Borkowski @oborkowski.bsky.social · Mar 29

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

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Reposted by Tom Dongmin Kim

OpenFold @openfold.io · Mar 28

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

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Reposted by Tom Dongmin Kim

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Mar 29

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

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Reposted by Tom Dongmin Kim

Colin Jackson @cjjackson.bsky.social · Mar 26

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…

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Reposted by Tom Dongmin Kim

ISCB News @iscb.bsky.social · Mar 18

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.

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Reposted by Tom Dongmin Kim

Bird account @dialecticbio.bsky.social · Dec 28

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

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Reposted by Tom Dongmin Kim

EMBL-EBI @ebi.embl.org · Mar 3

🚀 #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

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Reposted by Tom Dongmin Kim

Loren Williams @lorendw.bsky.social · Mar 8

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

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Reposted by Tom Dongmin Kim

Tanai Cardona @tanaicardona.bsky.social · Mar 7

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

2 7

Tom Dongmin Kim @tomdongmin.bsky.social · Mar 7

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

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

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Reposted by Tom Dongmin Kim

Michael Booth @drmikebooth.bsky.social · Mar 7

🚨 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

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Reposted by Tom Dongmin Kim

Olivier Borkowski @oborkowski.bsky.social · Mar 7

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

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