Kirill Medvedev
@kirillemedvedev.bsky.social
Assistant Professor @ucf.bsky.social
https://medvedev-lab.cs.ucf.edu/
Alumni @utswtxid.bsky.social
Computational Biology | Bionformatics | Cancer Biology
https://medvedev-lab.cs.ucf.edu/
Alumni @utswtxid.bsky.social
Computational Biology | Bionformatics | Cancer Biology
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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 ...
medvedev-lab.cs.ucf.edu
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
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
October 16, 2025 at 8:21 PM
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
Reposted by Kirill Medvedev
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 👇)
October 15, 2025 at 12:22 PM
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 👇)
Reposted by Kirill Medvedev
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/4nA8E6p
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.
go.nature.com
September 21, 2025 at 11:29 AM
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/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
September 16, 2025 at 9:14 PM
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
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
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 ...
medvedev-lab.cs.ucf.edu
August 12, 2025 at 3:43 PM
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
Reposted by Kirill Medvedev
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...
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...
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...
www.biorxiv.org
July 25, 2025 at 2:52 PM
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...
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...
Reposted by Kirill Medvedev
Molecular cat tweezers? 😺
July 12, 2025 at 4:12 AM
Molecular cat tweezers? 😺
Reposted by Kirill Medvedev
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:
Links evolutionary domain classes to ligand binding in PDB & AlphaFold human targets.
July 7, 2025 at 8:59 PM
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:
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
July 7, 2025 at 9:45 PM
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
Reposted by Kirill Medvedev
Computer algorithms have designed highly efficient synthetic enzymes from scratch
https://go.nature.com/3FLSiaS
https://go.nature.com/3FLSiaS
‘Remarkable’ new enzymes built by algorithm with physics know-how
Computer approach creates synthetic enzymes 100 times more efficient than those designed by AI.
go.nature.com
June 18, 2025 at 3:47 PM
Computer algorithms have designed highly efficient synthetic enzymes from scratch
https://go.nature.com/3FLSiaS
https://go.nature.com/3FLSiaS
Reposted by Kirill Medvedev
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! ⬇️
June 12, 2025 at 1:44 PM
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! ⬇️
Reposted by Kirill Medvedev
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
woodstock.img.cas.cz
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.
www.the-scientist.com
June 2, 2025 at 5:43 PM
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
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 😉
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 😉
May 14, 2025 at 4:57 PM
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 😉
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
May 5, 2025 at 4:05 PM
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
Reposted by Kirill Medvedev
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.
April 22, 2025 at 4:37 PM
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.
Reposted by Kirill Medvedev
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...
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...
April 17, 2025 at 7:11 PM
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...
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
"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...
"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...
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.
www.nature.com
April 11, 2025 at 4:53 PM
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...
"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...
Reposted by Kirill Medvedev
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
April 8, 2025 at 4:12 PM
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
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...
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...
Publishers trial paying peer reviewers — what did they find?
Two journals embarked on efforts to compensate reviewers, with different results.
www.nature.com
April 2, 2025 at 8:33 PM
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...
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...
Reposted by Kirill Medvedev
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
A 2023 #ScienceSignaling study solved the structure of this extracellular protein that plays an essential role in vision. Learn more: scim.ag/4gZdRRI
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.
scim.ag
February 27, 2025 at 5:25 PM
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
A 2023 #ScienceSignaling study solved the structure of this extracellular protein that plays an essential role in vision. Learn more: scim.ag/4gZdRRI
Reposted by Kirill Medvedev
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.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
the word irony is written on a white background
ALT: the word irony is written on a white background
media.tenor.com
February 22, 2025 at 10:19 AM
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.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
Reposted by Kirill Medvedev
More and more scientists are joining the ranks of fired federal workers—and fighting back through protests, appeals, and legal challenges.
Mass firings decimate U.S. science agencies
White House dismissals and rationale challenged by dismissed scientists and lawsuits
scim.ag
February 18, 2025 at 11:20 PM
More and more scientists are joining the ranks of fired federal workers—and fighting back through protests, appeals, and legal challenges.
Reposted by Kirill Medvedev
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
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
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 ...
scim.ag
February 18, 2025 at 3:08 PM
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
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