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Kirill Medvedev

@kirillemedvedev.bsky.social
64 followers 84 following 18 posts

Assistant Professor @ucf.bsky.social medvedevlab.org Alumni @utswtxid.bsky.social Computational Biology | Bionformatics | Cancer Biology

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Reposted by Kirill Medvedev
Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Kirill Medvedev @kirillemedvedev.bsky.social · 11/09/2026
💡New paper! Predicted off-targets for Seladelpar and Zanamivir with AlphaFold3 + MD, then tested the top 3. All inactive. For PPARγ, 4 of 5 AF3 models put the drug ~8 Å off - the only correct pose scored lowest confidence. Stability ≠ function. link.springer.com/article/10.1... #alphafold #boltz2
link.springer.com
Stable simulations do not guarantee functional engagement: a case study of off-target prediction for Seladelpar and Zanamivir - Journal of Computer-Aided Molecular Design
Identifying off-target interactions of approved drugs is important to anticipate side effects and uncover repurposing opportunities. Computational pipelines combining structural homology, structure pr...
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Kirill Medvedev @kirillemedvedev.bsky.social · 26/06/2026
@plos.org doi.org/10.1371/jour... We systematically investigated protein isoform variation impacts on drug-target interaction predictions. Our results showed that substituting canonical sequences with alternative isoforms causes substantial performance declines. @ucfcecs.bsky.social
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Kirill Medvedev @kirillemedvedev.bsky.social · 11/03/2026
Really excited to see our work @natmicrobiol.nature.com
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Reposted by Kirill Medvedev
Nature Microbiology @natmicrobiol.nature.com · 09/03/2026
Out Now! Bacterial Schlafen proteins mediate phage defence #MicroSky
go.nature.com
Bacterial Schlafen proteins mediate phage defence
Nature Microbiology, Published online: 09 March 2026; doi:10.1038/s41564-026-02277-8This study highlights that Schlafens are ancient, mechanistically conserved immune effectors that mediate antiviral immunity in organisms ranging from humans to bacteria.
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Kirill Medvedev @kirillemedvedev.bsky.social · 14/11/2025
www.cs.ucf.edu/2025/10/28/a...
cs.ucf.edu
Academic Upbringing in Siberia Inspires New Professor’s Career -
Kirill Medvedev's academic upbringing in Akademgorodok, Siberia, influenced his future career path, which led him to UCF.
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Kirill Medvedev @kirillemedvedev.bsky.social · 16/10/2025
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
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Reposted by Kirill Medvedev
Oded Rechavi @odedrechavi.bsky.social · 15/10/2025
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 👇)
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Reposted by Kirill Medvedev
Nature @nature.com · 21/09/2025
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
go.nature.com
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.
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Kirill Medvedev @kirillemedvedev.bsky.social · 16/09/2025
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
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Kirill Medvedev @kirillemedvedev.bsky.social · 12/08/2025
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
medvedev-lab.cs.ucf.edu
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 ...
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Reposted by Kirill Medvedev
Artem Nemudryi @artemnemudryi.bsky.social · 25/07/2025
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...
biorxiv.org
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...
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Reposted by Kirill Medvedev
Sergey Ovchinnikov @sokrypton.org · 12/07/2025
Molecular cat tweezers? 😺
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Reposted by Kirill Medvedev
AI x Bio Discovery @aixbiobot.bsky.social · 07/07/2025
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.
DrugDomain2.0: comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data BankFigure 1Figure 2Figure 3
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Kirill Medvedev @kirillemedvedev.bsky.social · 07/07/2025
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
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Reposted by Kirill Medvedev
Nature @nature.com · 18/06/2025
Computer algorithms have designed highly efficient synthetic enzymes from scratch go.nature.com/3FLSiaS
go.nature.com
‘Remarkable’ new enzymes built by algorithm with physics know-how
Computer approach creates synthetic enzymes 100 times more efficient than those designed by AI.
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Reposted by Kirill Medvedev
Oli Clarke @olibclarke.bsky.social · 12/06/2025
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! ⬇️
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.
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Reposted by Kirill Medvedev
Oded Rechavi @odedrechavi.bsky.social · 02/06/2025
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
the-scientist.com
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.
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Kirill Medvedev @kirillemedvedev.bsky.social · 14/05/2025
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 😉
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Kirill Medvedev @kirillemedvedev.bsky.social · 05/05/2025
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
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Reposted by Kirill Medvedev
Trends in Pharmacological Sciences @cp-trendspharma.bsky.social · 22/04/2025
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.
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Reposted by Kirill Medvedev
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/04/2025
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...
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Kirill Medvedev @kirillemedvedev.bsky.social · 11/04/2025
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...
nature.com
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.
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Reposted by Kirill Medvedev
RCSB Protein Data Bank @rcsbpdb.bsky.social · 08/04/2025
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
ApoB100 (orange) wraps around the LDL particle like a belt. LDL receptors (pink and purple) bind to multiple locations on ApoB100 (PDB 9BDT).
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Kirill Medvedev @kirillemedvedev.bsky.social · 02/04/2025
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...
nature.com
Publishers trial paying peer reviewers — what did they find?
Two journals embarked on efforts to compensate reviewers, with different results.
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Reposted by Kirill Medvedev
Science Magazine @science.org · 27/02/2025
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
scim.ag
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.
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Reposted by Kirill Medvedev
Jeremy Berg @jeremymberg.bsky.social · 22/02/2025
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.
media.tenor.com
the word irony is written on a white background
ALT: the word irony is written on a white background
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Reposted by Kirill Medvedev
Science Magazine @science.org · 18/02/2025
More and more scientists are joining the ranks of fired federal workers—and fighting back through protests, appeals, and legal challenges.
scim.ag
Mass firings decimate U.S. science agencies
White House dismissals and rationale challenged by dismissed scientists and lawsuits
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Reposted by Kirill Medvedev
Science Magazine @science.org · 18/02/2025
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
scim.ag
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 ...
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Kirill Medvedev @kirillemedvedev.bsky.social · 17/02/2025
Excited to share my recent research related to interactions between small molecule drugs and protein domains. @biophysicalsoc.bsky.social #bps2025 #computationalbiology #bioinformatics #drugdiscovery
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Reposted by Kirill Medvedev
Prash Singh @prash-singh.bsky.social · 05/01/2025
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
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Kirill Medvedev @kirillemedvedev.bsky.social · 28/01/2025
📜 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.
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