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Marian Novotny @majek.bsky.social · 16d

Congratulations, Vaclav!

Vaclav Veverka @vaclav-veverka.bsky.social · 17d

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

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Marian Novotny @majek.bsky.social · Sep 4

Huge congratulations!

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Marian Novotny @majek.bsky.social · Aug 27

Congratulations! Exciting work!

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Reposted by Marian Novotny

Alessandro Nascimento @asnascimento.bsky.social · Jul 8

👇🏾👇🏾👇🏾

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Marian Novotny @majek.bsky.social · Jul 9

Congratulations!

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Reposted by Marian Novotny

Pedro Beltrao @pedrobeltrao.bsky.social · Jul 5

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.

bioRxiv SysBio @biorxiv-sysbio.bsky.social · Jul 5

Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3 https://www.biorxiv.org/content/10.1101/2025.07.01.662654v1

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Marian Novotny @majek.bsky.social · Jun 23

Great news! Stay safe

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Marian Novotny @majek.bsky.social · Jun 19

Thank you, guys, for joining us - you made our meeting much better! It was a pure pleasure to have you!!!

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Marian Novotny @majek.bsky.social · Jun 19

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

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Marian Novotny @majek.bsky.social · Jun 10

@vaclav-veverka.bsky.social presents his phase seperation doubts #theconferencetoendallconferences #TCTeAC

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Marian Novotny @majek.bsky.social · Jun 10

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

Radoslav Krivak @rdkbio.bsky.social · Jun 10

🚀 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

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Marian Novotny @majek.bsky.social · May 29

We did expect that! Congratulations, Honzo!

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Reposted by Marian Novotny

Deník N @denikn.cz · May 23

„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

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Marian Novotny @majek.bsky.social · May 2

Congratulations @javierutges.bsky.social !

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Marian Novotny @majek.bsky.social · Apr 23

Jalview team strikes again! Congratulations!

Dr Javier Sánchez Utgés @javierutges.bsky.social · Apr 23

#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!

Jalview @jalview.bsky.social · Apr 23

💡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...

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Marian Novotny @majek.bsky.social · Mar 27

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!

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Marian Novotny @majek.bsky.social · Mar 4

@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!

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Marian Novotny @majek.bsky.social · Feb 20

See you there!

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Marian Novotny @majek.bsky.social · Feb 16

Thank you for this! It explains many observations i could not comprehend!

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Marian Novotny @majek.bsky.social · Feb 8

Congratulations, i wonder whether the current tools can move ligands to right places…

Peter Škrinjar @peterskrinjar.bsky.social · Feb 8

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)

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

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Marian Novotny @majek.bsky.social · Feb 6

Counterintuitive

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Feb 6

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...

Text from the paper discussing various manual adjustments and choices of the hydrophobicity scale

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Marian Novotny @majek.bsky.social · Feb 5

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

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Reposted by Marian Novotny

Česká společnost ornitologická @birdlife.cz · Jan 31

🪶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

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Marian Novotny @majek.bsky.social · Jan 24

An important extension ofPyMOL by Rafi’s @rnajmanovich.bsky.social group

Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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.

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Jan 24

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

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Marian Novotny @majek.bsky.social · Jan 23

Diky moc!