Kirill Medvedev

Really excited to be part of these Research Talks at @ucf.bsky.social Will be sharing some stories 🙂: "From Protein Domains to Cancer Subtypes: Harnessing the Power of Classification Algorithms to Advance Biology" #UCF #computerscience #bioinformatics #computationalbiology

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

World's first AI-designed viruses a step towards AI-generated life Nature - Scientists used AI to write coherent viral genomes, using them to synthesize bacteriophages capable of killing resistant strains of bacteria.

Scientists have created the first ever viruses designed by AI, and they’re capable of hunting down and killing strains of E. coli

go.nature.com/4nA8E6p

DrugDomain 2.0 (drugdomain.cs.ucf.edu) paper is out @csbj.org: doi.org/10.1016/j.cs... The new version of DB is an updated comprehensive resource, that extends earlier releases by linking evolutionary domain classifications to ligand binding events across the entire Protein Data Bank #bioinformatics

Join Computational Structural Biology | Cancer Bioinformatics | Digital Pathology. Medvedev Lab will open in August 2025 in the [Department of Computer Science](https://www.cs.ucf.edu/) at the [University ...

I’m happy to share that I’m starting a new position as Assistant Professor and Medvedev lab is open at the Department of Computer Science @ucf.bsky.social I am seeking motivated PhD students to join my lab. Hiring details: medvedev-lab.cs.ucf.edu/join/ Please repost 🙂 #hiring #bioinformatics

Bacterial Schlafens mediate anti-phage defense Human Schlafen proteins restrict viral replication by cleaving tRNA, thereby suppressing protein synthesis. Although the ribonuclease domain of Schlafen proteins is conserved across all domains of lif...

First preprint from the Nemudryi Lab! 🍾

In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages.

www.biorxiv.org/content/10.1...

Molecular cat tweezers? 😺

DrugDomain2.0: comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank

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DrugDomain2.0: comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank [new]
DrugDomain2.0:
Links evolutionary domain classes to ligand binding in PDB & AlphaFold human targets.

DrugDomain v2.0 is out - drugdomain.cs.ucf.edu The database reports the interactions of structural protein domains with a wide array of small organic (including drugs) and inorganic compounds, covering the full breadth of the Protein Data Bank. doi.org/10.1101/2025... #drugdiscovery #alphafold

‘Remarkable’ new enzymes built by algorithm with physics know-how Computer approach creates synthetic enzymes 100 times more efficient than those designed by AI.

Computer algorithms have designed highly efficient synthetic enzymes from scratch

https://go.nature.com/3FLSiaS

At left, a reconstruction of the vault cap with C39 symmetry imposed; at right, the reconstruction after identifying the correct symmetry, with the three non-equivalent protomers highlighted.

1/x New story - the structure of the Vault cap, at 2.3Å! Matching a beautiful preprint from @sjorsscheres.bsky.social, we show that the cap of the vault particle has C13 symmetry, in contrast to the 39-fold symmetry of the body. Study lead by talented postdoc @huanli00.bsky.social from my group! ⬇️

A Scientific Conference to End All Conferences With walk-up songs, bold ideas, and a festival atmosphere, like-minded researchers band together to reshape scientific meetings.

One week from now!!! The craziest scientific conference ever www.the-scientist.com/a-scientific... @svobodalab.bsky.social @paveltomancak.bsky.social @zernickagoetz.bsky.social @itaiyanai.bsky.social @natanellae.bsky.social see more here
woodstock.img.cas.cz

Thrilled to share that I'll be joining @ucf.bsky.social as an Assistant Professor.
Medvedev Lab (medvedev-lab.cs.ucf.edu) will open in August 2025. Our work will address critical biological questions in Structural and Cancer Biology. Stay tuned 😉

We used AI to study how post-translational modifications (PTMs) affect drug binding and protein structure. Using AF3, RFAA and Chai-1, we generated > 14,000 models with > 6,000 of ligand-related PTMs. Paper is out in J. of Chemoinformatics rdcu.be/ekFlo #drugdiscovery #alphafold #bioinformatics #AI

The cover of the April issue of @cp-trendspharma.bsky.social. Gregory Howard and William Tansey review the current status, challenges, and future prospects of cancer treatments that target the ribosome. Aberrant ribosome production and function are hallmarks of cancer.

AlphaFold is amazing but gives you static structures 🧊

In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃

Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...

How a junk-food splurge can change your brain activity A short bout of indulgence in fatty, sugary snacks leads to lingering brain-activity changes ― even if it does not cause weight gain.

How a junk-food splurge can change your brain activity

"Five days of indulging in chocolate bars, crisps and other junk foods can lead to lingering changes in brain activity similar to those seen in people who have type 2 diabetes"
www.nature.com/articles/d41...

ApoB100 (orange) wraps around the LDL particle like a belt. LDL receptors (pink and purple) bind to multiple locations on ApoB100 (PDB 9BDT).

April's Molecule of the Month at PDB-101 looks at Apolipoprotein B-100 and LDL Receptor, important structures that help us better understand how "bad" cholesterol works in the body

Publishers trial paying peer reviewers — what did they find? Two journals embarked on efforts to compensate reviewers, with different results.

Way to go!
This month, two journals released data from their own experiments that suggest that offering payments of around US$250 to researchers who review manuscripts speeds up the process, without affecting the quality of reviews

www.nature.com/articles/d41...

Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179 The structure of the orphan GPCR GPR179 bound to the extracellular matrix component pikachurin is solved.

What do you get when #NationalProteinDay and #NationalPokémonDay meet? Pikachurin. ⚡⁠
⁠
A 2023 #ScienceSignaling study solved the structure of this extracellular protein that plays an essential role in vision.⁠ Learn more: scim.ag/4gZdRRI

the word irony is written on a white background ALT: the word irony is written on a white background

I have been trying to find the time to move away from the polical hellscape we find ourselves in to finish and share a bluetorial about science.

This helps me remember what this is all about.

Ironically, it is about the treatment of pain.

Today, the NVIDIA healthcare and life sciences team launched Evo 2 -- a powerful foundation model for DNA across all domains of life, developed in collaboration with @arcinstitute.org and @stanforduniversity.bsky.social. More in 🧵

Mass firings decimate U.S. science agencies White House dismissals and rationale challenged by dismissed scientists and lawsuits

More and more scientists are joining the ranks of fired federal workers—and fighting back through protests, appeals, and legal challenges.

Computational design of serine hydrolases The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of ...

New research in Science represents a notable step forward in designing enzymes from scratch.

With a new approach, researchers designed an enzyme that uses a covalent intermediate to catalyze a two-step reaction, analogous to what many proteases do when breaking apart proteins. scim.ag/41kZBOI

Excited to share my recent research related to interactions between small molecule drugs and protein domains. @biophysicalsoc.bsky.social #bps2025 #computationalbiology #bioinformatics #drugdiscovery

Posting it on Bluesky to save the post:
My grandfather built motors that powered big machines. In a lab not so different from his workshop, my colleagues and I uncovered the assembly of the bacterial motor. www.nature.com/articles/s41... @natureportfolio.bsky.social #MolecularNodes #Science #STEM

💡We mapped identified PTMs to structural domains in the ECOD database and report all data at DrugDomain database (prodata.swmed.edu/DrugDomain/), which offers the first large-scale collection of PTM-modified protein models with docked small molecules.
#AIinDrugDiscovery #ProteinBinding #AlphaFold

💡 We also compared different AI tools for modeling PTMs in protein structures and found that Chai-1 and RoseTTAFold All-Atom were particularly effective in predicting the effects of PTMs on drug binding.

💡 Using AlphaFold3, RoseTTAFold All-Atom and Chai-1, we generated more than 14000 models with over 6000 of ligand-related PTMs. We discovered that phosphorylation of NADPH-Cytochrome Reductase leads to substantial structural disruption in the binding pocket, potentially hindering protein function

📜 Our new preprint is out: www.biorxiv.org/content/10.1...

💡 We explored the role of post-translational modifications (PTMs) in modulating drug binding, with a focus on understanding the structural consequences of PTMs using advanced AI methods.