Marian Novotny
@majek.bsky.social
Proud dad, structural bioinformatician, cook, birdwatcher and skater
Congratulations, Vaclav!
How do flexible regions of histone chaperones team up to handle histones? Together with Fred Winston’s lab
@harvardmed.bsky.social, we reveal new insights in our study just out in Mol Cell. Hats off to James Warner and Vanda Lux @iocbprague.bsky.social for their key contributions! dlvr.it/TNB145
@harvardmed.bsky.social, we reveal new insights in our study just out in Mol Cell. Hats off to James Warner and Vanda Lux @iocbprague.bsky.social for their key contributions! dlvr.it/TNB145
September 22, 2025 at 2:00 PM
Congratulations, Vaclav!
Reposted by Marian Novotny
Reposted by Marian Novotny
Great work from Horia Todor in Carol Gross's lab showing it's possible to predict complexes in "competition" pools in AF3 resulting in the first all-by-all prediction for a species. After length correcting the ipTM score predicts well known interactions and correlating ipTM vectors also has value.
Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3 https://www.biorxiv.org/content/10.1101/2025.07.01.662654v1
July 5, 2025 at 5:14 AM
Great work from Horia Todor in Carol Gross's lab showing it's possible to predict complexes in "competition" pools in AF3 resulting in the first all-by-all prediction for a species. After length correcting the ipTM score predicts well known interactions and correlating ipTM vectors also has value.
Fantastic to work with so many talented people! today at departmental conference of cell biology department of @sciencecharles.bsky.social . Many thanks to our guests from Israel for joining us and sharing their results and time with us
June 19, 2025 at 9:06 AM
Fantastic to work with so many talented people! today at departmental conference of cell biology department of @sciencecharles.bsky.social . Many thanks to our guests from Israel for joining us and sharing their results and time with us
@vaclav-veverka.bsky.social presents his phase seperation doubts #theconferencetoendallconferences #TCTeAC
June 10, 2025 at 5:38 PM
@vaclav-veverka.bsky.social presents his phase seperation doubts #theconferencetoendallconferences #TCTeAC
P2Rank has a new version - you can even see a ligand bound to the identified pocket now - please , check it out and look at our NAR paper for a summary of the upgrades
🚀 Our paper on the updated PrankWeb, a web app for protein binding site prediction using P2Rank, is out in
@narjournal.bsky.social. Now with docking integration!
👨💻 Try it: prankweb.cz
📄 Paper: doi.org/10.1093/nar/...
💻 GitHub: github.com/cusbg/prankweb
Developed at @cusbg.bsky.social
@narjournal.bsky.social. Now with docking integration!
👨💻 Try it: prankweb.cz
📄 Paper: doi.org/10.1093/nar/...
💻 GitHub: github.com/cusbg/prankweb
Developed at @cusbg.bsky.social
June 10, 2025 at 3:38 PM
P2Rank has a new version - you can even see a ligand bound to the identified pocket now - please , check it out and look at our NAR paper for a summary of the upgrades
Reposted by Marian Novotny
„Hledání života ve vesmíru je pro mě asi největší vědecké dobrodružství,“ říká jedna z nejúspěšnějších českých vědkyň, biochemička a astrobioložka Klára Hlouchová. Zkoumá otázky původu a evoluce proteinů. Co ještě není, a co už je schopno života?
Nález života ve vesmíru by s námi mohl pěkně zamávat, říká astrobioložka. Zkoumá vznik života i slepé uličky
Co ještě není, a co už je schopno života? A jak by mohl vypadat život ve vesmíru? Biochemička a astrobioložka Klára Hlouchová zkoumá otázky původu a evoluce proteinů. A otázky života, vesmíru a tak…
denikn.cz
May 23, 2025 at 6:29 PM
„Hledání života ve vesmíru je pro mě asi největší vědecké dobrodružství,“ říká jedna z nejúspěšnějších českých vědkyň, biochemička a astrobioložka Klára Hlouchová. Zkoumá otázky původu a evoluce proteinů. Co ještě není, a co už je schopno života?
Jalview team strikes again! Congratulations!
#Jalview goes the extra mile! Remember the integration with @chimerax.ucsf.edu or #PyMOL? Well, you can use these viewers to inspect #AlphaFold confidence scores #pLDDT and #PAE in multiple #sequence alignment and #structure!
Multiple structure prediction confidence analysis made easy with Jalview!
Multiple structure prediction confidence analysis made easy with Jalview!
💡Protein lovers - a brand NEW video exploring AlphaFold's pLDDT score in Jalview is out! Find out how you can select, hide and colour your alignments using this 3D structure prediction confidence metric.
▶️ Watch the full video here: www.youtube.com/watch?v=WVCM...
▶️ Watch the full video here: www.youtube.com/watch?v=WVCM...
April 23, 2025 at 6:46 PM
Jalview team strikes again! Congratulations!
We are grateful and fortunate to have Sameer Velankar, the head of @pdbeurope.bsky.social, to start first ever @elixircz.bsky.social phd conference. Thank you RSJ and @elixircz.bsky.social for general support!
March 27, 2025 at 12:19 PM
We are grateful and fortunate to have Sameer Velankar, the head of @pdbeurope.bsky.social, to start first ever @elixircz.bsky.social phd conference. Thank you RSJ and @elixircz.bsky.social for general support!
@elixircz.bsky.social is celebrating 10th anniversary today! Jiri Vondrasek is in his summary acknowledging Janet Thornton and her contribution to founding of Elixir. Thank you!
March 4, 2025 at 1:12 PM
@elixircz.bsky.social is celebrating 10th anniversary today! Jiri Vondrasek is in his summary acknowledging Janet Thornton and her contribution to founding of Elixir. Thank you!
Congratulations, i wonder whether the current tools can move ligands to right places…
Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 7:42 PM
Congratulations, i wonder whether the current tools can move ligands to right places…
Counterintuitive
There are lots of hydrophobicity scales and perhaps the most well known and used is that from Kyte & Doolittle
If you ever use that scale, I recommend reading the original paper and noting the authors' pragmatism and honesty about manual adjustments and using intuition
doi.org/10.1016/0022...
If you ever use that scale, I recommend reading the original paper and noting the authors' pragmatism and honesty about manual adjustments and using intuition
doi.org/10.1016/0022...
February 6, 2025 at 9:42 PM
Counterintuitive
Things are often obvious, but sometimes less so. It is true also for small things like ligand-binding sites. In this work, our @cusbg.bsky.social group presents a new dataset designed for cryptic-binding site predictons - happy, to be part of this: academic.oup.com/bioinformati...
CryptoBench: cryptic protein–ligand binding sites dataset and benchmark
AbstractMotivation. Structure-based methods for detecting protein–ligand binding sites play a crucial role in various domains, from fundamental research to
academic.oup.com
February 5, 2025 at 10:43 AM
Things are often obvious, but sometimes less so. It is true also for small things like ligand-binding sites. In this work, our @cusbg.bsky.social group presents a new dataset designed for cryptic-binding site predictons - happy, to be part of this: academic.oup.com/bioinformati...
Reposted by Marian Novotny
🪶Nečekané a vzácné pozorování pelikána bílého ve čtvrtek v ptačím parku Kosteliska na Hodonínsku. Pták byl v dobré kondici, bez chovatelských kroužků a často ladně přeletoval a kroužil.
Jedná se již o 209. ptačí druh pozorovaný v ptačím parku ČSO Kosteliska.
Foto: Ondřej Ryška
Jedná se již o 209. ptačí druh pozorovaný v ptačím parku ČSO Kosteliska.
Foto: Ondřej Ryška
January 31, 2025 at 9:56 AM
🪶Nečekané a vzácné pozorování pelikána bílého ve čtvrtek v ptačím parku Kosteliska na Hodonínsku. Pták byl v dobré kondici, bez chovatelských kroužků a často ladně přeletoval a kroužil.
Jedná se již o 209. ptačí druh pozorovaný v ptačím parku ČSO Kosteliska.
Foto: Ondřej Ryška
Jedná se již o 209. ptačí druh pozorovaný v ptačím parku ČSO Kosteliska.
Foto: Ondřej Ryška
An important extension ofPyMOL by Rafi’s @rnajmanovich.bsky.social group
Our newest preprint is out. A PyMOL plugin giving access to a broad suite of high-performance, fast, and easy to use methods for virtual screening (50K molecules/h), docking, analysis of molecular interactions, dynamics, engineering permitting complex workflows.
NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities https://www.biorxiv.org/content/10.1101/2025.01.23.634566v1
January 24, 2025 at 9:34 PM
An important extension ofPyMOL by Rafi’s @rnajmanovich.bsky.social group
Two of our colleagues at the department of cell biology @sciencecharles.bsky.social just received Neuron prize. Congratulations, Klara Hlouchova and Jan Cerny. www.nadaceneuron.cz/ceny-neuron-...
Ceny Neuron 2024
Nadace Neuron udělila prestižní vědecká ocenění excelentním vědkyním a vědcům
www.nadaceneuron.cz
January 19, 2025 at 7:55 PM
Two of our colleagues at the department of cell biology @sciencecharles.bsky.social just received Neuron prize. Congratulations, Klara Hlouchova and Jan Cerny. www.nadaceneuron.cz/ceny-neuron-...
Welcome a new doctor! My student has successfuly defended his thesis on diversity of ligand binding sites today! Congratulations, Christos Feidakis!
January 16, 2025 at 6:26 PM
Welcome a new doctor! My student has successfuly defended his thesis on diversity of ligand binding sites today! Congratulations, Christos Feidakis!
Reposted by Marian Novotny
AF3 BEST METHOD followed by cluspro but also some conversion errors
December 3, 2024 at 5:46 PM
Congratulations, Klara! Look forward to our next project!
Klára Hlouchová from the Department of Cell Biology received an ERC Consolidator grant!👋 A groundbreaking ERC-funded project aims to create 'LIFE-19'—a bacterial strain using just 19 amino acids instead of 20 🧬. Congratulations! #SyntheticBiology #ERCCoG
📌 1url.cz/U1Zvc
📌 1url.cz/U1Zvc
December 3, 2024 at 12:47 PM
Congratulations, Klara! Look forward to our next project!
Reposted by Marian Novotny
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Stereochemistry in the disorder–order continuum of protein interactions - Nature
Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.
www.nature.com
November 27, 2024 at 8:31 PM
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Congratulations to Honza and his great team!
🎉👏 Dr. Jan Dobeš from our faculty at has won the INVENCE #award at Česká hlava! 🔬 His research reveals how the #immune system fights #yeast infections. 🌟 Congratulations on this prestigious recognition!
📌 natur.cuni.cz/en/news/5872...
📌 natur.cuni.cz/en/news/5872...
November 22, 2024 at 12:02 PM
Congratulations to Honza and his great team!
Happy to wait!
#GoodThingsComeToThoseWait Sorry it's taking us a while. Promise that the wait will be well worth it! #OpenFold3 Love all the great work that's already been done #HelixFold3 #Ligo #Chai1 #Protenix #Boltz1
November 20, 2024 at 7:51 PM
Happy to wait!
Highly recommended!
join us at #8ADD
At the end of January we organize hybrid 8th Advanced in silico drug design workshop -
registration is open both onsite and online
www.kfc.upol.cz/8add #chemsky #compchemsky #biosky 🧪💊🧬🖥️
registration is open both onsite and online
www.kfc.upol.cz/8add #chemsky #compchemsky #biosky 🧪💊🧬🖥️
November 19, 2024 at 12:51 PM
Highly recommended!
Reposted by Marian Novotny
Trying to collect scientists in/from Czech Republic who are here. Let me know who should I add!
go.bsky.app/Q4XavnF
go.bsky.app/Q4XavnF
November 19, 2024 at 11:06 AM
Trying to collect scientists in/from Czech Republic who are here. Let me know who should I add!
go.bsky.app/Q4XavnF
go.bsky.app/Q4XavnF