Piotr Draczkowski

Bioinformatician / Research engineer in structural biology @SciLifeLab.
Outdoor addicted.
Old-fashioned analogue photography enthusiast.

[IMol @IMol_Institute]

A new @IMol_Institute study in Science Advances sheds light on mitochondrial protein import.

https://t.co/6eHgQbq13v

Huge credit to this outstanding team of co-authors!

[Piotr Draczkowski @PDraczkowski]

A special thanks to @asibc512, Szu-Ni Chen, Ting Chen, Yong-Sheng Wang, and Yuan-Chih Chang for making this possible.

[Piotr Draczkowski @PDraczkowski]

If you're curious about how cells quickly eliminate misfolded proteins produced under proteotoxic stress or during cell cycle progression, check out our latest article in @NatureComms
https://t.co/LPkcLmvrr5

[Piotr Draczkowski @PDraczkowski]

It has been a long but incredibly valuable journey, filled with ups and downs, culminating in an exhausting publishing process. However, thanks to the tremendous efforts of all the coauthors, our publication is finally out!

[Piotr Draczkowski @PDraczkowski]

In this study, we enhance the structural understanding of the ubiquitin code by revealing previously unseen K11/K48-branched Ub chain topology and its recognition by the proteasome.

[danny hsu @asibc512]

What a day! We published two papers describing the lives of proteins from Alpha https://t.co/Jd3tWEktbZ to Omega https://t.co/y4BfTJk0B5

Seeing these processes through the lens of structural biology is so satisfying

[danny hsu @asibc512]

@PDraczkowski serendipitously found the K11/K48 branch, which is confirmed by Ub-AQUA and Ub-clipping. Amazing support from our #cryoEM and #proteomics MS core at @AcademiaSinica

[Max Planck Institute of Biophysics @MPIbp]

📣 Job alert! Our partner group, the Dioscuri Centre for Modeling of Posttranslational Modifications
@BioPhysMatt, is seeking a talented individual in the field of #ComputationalBiophysics. Apply ✏️✅! #AssistantProfessor 👉 https://t.co/wP0FP4MJ3o

[Piotr Draczkowski @PDraczkowski]

@MariuszCzC Brilliant work! Congrats!

[danny hsu @asibc512]

Very pleased to know that our recent work on hCoV-229E S:hAPN recognition has been highlighted by Nature Communications alongside the work of the newly minted Nobel Prize laureate David Baker https://t.co/cQJ62Zi1eu

[Biology+AI Daily @BiologyAIDaily]

ESMAdam: a plug-and-play all-purpose protein ensemble generator

1. ESMAdam introduces a versatile framework for protein ensemble generation, bridging gaps in high-throughput applications. Leveraging the pretrained ESMFold model and Adam optimization, it excels in efficiency and adaptability compared to traditional methods like molecular dynamics simulations.

2. The method supports a wide range of tasks, including conditional ensemble generation, CG-to-all-atom backmapping, binding mode exploration for protein complexes, and reconstructing 3D structures from cryo-EM images.

3. A key innovation is ESMAdam's reliance on optimizing protein embeddings in a continuous space. Unlike deep generative models, ESMAdam requires no retraining, allowing it to accommodate diverse structural constraints with minimal computational overhead.

4. In protein complex studies, ESMAdam identified metastable binding states previously undetected by molecular dynamics simulations, highlighting its potential for novel discovery in protein-protein interactions.

5. Cryo-EM integration demonstrates ESMAdam's robustness under noisy conditions. It reconstructs conformational ensembles while retaining accuracy in secondary structure prediction, even with significant noise levels.

6. The model achieves Boltzmann-distributed conformations, a feat previously challenging without physics-intensive simulations. It enhances studies on protein dynamics, stability, and interactions.

7. Future directions include reducing computational demands via techniques like LoRA for broader accessibility. ESMAdam positions itself as a critical tool for advancing structural biology and computational protein design.

📜Paper: https://t.co/W84B99ka4o

#ProteinDesign #AI #StructuralBiology #ComputationalBiology #ESMAdam

[Piotr Draczkowski @PDraczkowski]

This is exciting and opens new avenues for studying the proteasome-ubiquitin system. I am now awaiting K11 ubiquitin-specific probes ;)
https://t.co/t5pDwmdBzW

[Piotr Draczkowski @PDraczkowski]

Here’s a brief teaser for our latest preprint reporting the first structures of the K11/K48-branched Ub chain bound to the human proteasome:
https://t.co/illzy1JT4X
Check the full text for more details:
https://t.co/D9BMaW7poF

Thx to @asibc512 for making this possible!

[danny hsu @asibc512]

Our preprint on the first glimpse of how the human proteasome recognizes a K11/K48-branched ubiquitin chain is out. This work reveals a new multivalent ubiquitin binding mode by the proteasome that could serve as priority checkin signal for proteolysis.

https://t.co/Sk2ERBDb9B

[IMol @IMol_Institute]

Call for AMBER is now open and closes on September 6th. Prof. @A_Chacinska is seeking 2 postdoctoral researchers for 2 projects in structural biology, and molecular cell biology and proteomics.

Link to the project website: https://t.co/DsUWs1LSeJ @FNP_org_pl @PAN_akademia

[IMol @IMol_Institute]

How proteins are imported into human mitochondria? Read the latest publication from @A_Chacinska lab. Find out how Klaudia Maruszczak and @PDraczkowski used computational tools to get first architectural insights into these processes.

@NCN_PL

[Hanjin Liu @liu_hanjin]

Anyone ever needs a command palette in ChimeraX?

[Piotr Draczkowski @PDraczkowski]

@emollick AF3 is amazing and a real game changer but in terms of the interface nothing spectacular. What you showed is just a protein structure, distogram, and the protein sequence. Nothing new.

[Piotr Draczkowski @PDraczkowski]

Everyone (including me :) is hyped up about the new AF3 today, so let’s mix it up with some other cool science updates from yesterday:

[NASA Webb Telescope @NASAWebb]

The floor is lava! 🔥

Webb may have detected atmospheric gasses around molten 55 Cancri e, 41 light years from Earth. It’s the best evidence to date for a rocky planet with an atmosphere outside our solar system! https://t.co/8pl9VAIS1M

[Piotr Draczkowski @PDraczkowski]

Love it :D
@wojtek_pokrzywa have an idea to level up the difficulty: how about adding branched K11/K48 Ub chains into the game scenario? ;D

[Wojciech Pokrzywa @wojtek_pokrzywa]

Check out our game, DEGRADATOR! 🎮 Designed to popularize and educate on the ubiquitin-proteasome system and PROTACs. Perfect for kids 12+ but not only 😉 Dive into 10 fun levels to explore protein degradation. Available on Google Play and https://t.co/TMiwcfLi9M 🚀