Eva Smorodina @EvaSmorodina Twitter profile

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Eva Smorodina

@EvaSmorodina

27 days

Happy to have my work featured on the cover of @TheAbSociety calendar and mAbs journal!

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Eva Smorodina

@EvaSmorodina

4 months

Some observations from my very brief #AlphaFold3 (AF3) benchmarking: AF3 is good for globular proteins, soluble proteins, conserved proteins, RNA/DNA-protein complexes, etc. AF3 is bad for IDPs, protein-protein complexes, antibodies, protein-switches, membrane proteins, etc.

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Eva Smorodina

@EvaSmorodina

2 years

Very happy to share our review "Protein Design: From the Aspect of Water Solubility and Stability" published in @ACSChemRev !

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Eva Smorodina

@EvaSmorodina

5 months

Schrödinger's PyMOL 3 is impressive. Creating movies and adjusting the lighting has become significantly easier. For example, the attached video took only a few minutes compared to the hours I previously spent with PyMOL 2 crafting all the pretty scenes and interpolations!

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Eva Smorodina

@EvaSmorodina

11 months

Antibody design (and more) with copilot. Soon, you'll be able to try it. Don't miss the chance to be among the first!

Kathy Y. Wei, Ph.D.

@KathyYWei1

11 months

Design a protein with 310 CoPilot

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Eva Smorodina

@EvaSmorodina

4 months

I'm benchmarking #AlphaFold3 's ability to predict biomolecular structures. If you have any specific protein/RNA/DNA/complex in mind, feel free to leave them in the comments. Thanks in advance!

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Eva Smorodina

@EvaSmorodina

3 years

Our new review now in mAbs! 💫🎉

GreiffLab 💻🔬💊

@victorgreiff

3 years

Very happy that our review on the "Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies" is finally out.

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Eva Smorodina

@EvaSmorodina

10 months

Had a wonderful time at @NeurIPSConf , @workshopmlsb , and @genbio_workshop ! Met many people in person whom I've known before only online. Exciting talks about new advances in molecular docking and protein design using mostly LLMs, diffusion, and flow matching

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Eva Smorodina

@EvaSmorodina

2 years

My image is on the cover of @ACSChemRev ! #sciart

Chemical Reviews

Genetic code expansion (GCE) breakthroughs over the past decade have revolutionized synthetic biology, protein engineering, material science, and medicine by enabling the creation of synthetic...

pubs.acs.org

Chemical Reviews

@ACSChemRev

2 years

On the cover: an artistic rendition of α-helical proteins such as #GPCRs as the major components, together with water molecules, long fibrous amyloids comprised by cross-α and cross-β structures & high-order molecular assemblies to form waves & capsules:

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Eva Smorodina

@EvaSmorodina

2 months

Our paper about biophysical cartography of antibody developability parameters is finally out in @CommsBio ! Computational modeling of antibody structures is covered in the supplementary file. All structural data is on Zenodo.

Structural Data for the Antibody Developability Manuscript: Cartography of Developability Landsca...

Here is the additional structural data (predicted models and MD trajectories) for the "Cartography of the Developability Landscapes of Native and Human-Engineered Antibodies" manuscript. Please cite...

zenodo.org

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Eva Smorodina

@EvaSmorodina

1 year

Thrilled to announce that I've reached 100 Google Scholar citations! I'm incredibly grateful for my amazing co-authors, supervisors, and friends who made this achievement possible 🎊🎓

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Eva Smorodina

@EvaSmorodina

10 months

The copilot is finally out! Sign up for the waiting list to get early access: #ai #proteindesign #copilot #ml #proteins #biotech

kooshiar

@kooshiar

10 months

Our copilot for protein engineering is live! #ai

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Eva Smorodina

@EvaSmorodina

3 years

What are the most beautiful/interesting protein structures you know? Please write your favorite PDBs!

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Eva Smorodina

@EvaSmorodina

11 months

Our work with @strodellab is published in Proteins: Structure, Function, and Bioinformatics! In the paper, you can find out more about how different ion types and concentrations influence amyloid structure and behavior.

Effects of ion type and concentration on the structure and aggregation of the amyloid peptide...

Among the various factors controlling the amyloid aggregation process, the influences of ions on the aggregation rate and the resulting structures are important aspects to consider, which can be...

onlinelibrary.wiley.com

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Eva Smorodina

@EvaSmorodina

3 years

Many thanks for Copenhagen Bioinformatics Hackathon 2021 Protein Edition! It was amazing! 🤩 @CBioVikings @biolib @mark_fingerhuth @jsci @proteinqure

Evgenia Elizarova

@ZhenyaElizarova

3 years

Some challenging days spent on 3D protein structures, ML and with the best team! Congrats to us🥳(and Mentor's Pick Award too🤩) Thank you guys! And of course thanks to mentors and organizers! @NAzbukina @EvaSmorodina @ZinkevichA @anna_kamysheva #BioHackathon2021

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Eva Smorodina

@EvaSmorodina

4 years

Click-chemistry as aptamers' properties modulation tool #Lomonosov2020 , #Lomonosov2020Bioinf

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Eva Smorodina

@EvaSmorodina

11 months

Finally, our work has been published as a preprint 🎉

Habib Bashour

@HabibBashour

11 months

(1/10) Our work on antibody developability is out! We present a cartography of the developability landscapes of the native and human-engineered antibodies. This study was a team effort of @HabibBashour @EvaSmorodina @pariset_matteo , and @Jahn_Zhong

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Eva Smorodina

@EvaSmorodina

5 months

Had a wonderful time in Leiden at the free energy calculations workshop. Many great speakers shared their views on the current development of the field. Overall, there were lots of insights on state-of-the-art approaches used in drug design. #alchemy2024 #drugdesign2024

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Eva Smorodina

@EvaSmorodina

2 years

Super beautiful 😍

Mike Tyka (@[email protected])

@mtyka

2 years

I'm very happy to finally reveal this sculpture. Two years in the making (together with ) and under embargo as it was a surprise for my former postdoc adviser David Baker.

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Eva Smorodina

@EvaSmorodina

4 months

AF3 can't predict biomolecules with changing conformations or flexible and disordered regions whose structure depends a lot on the environment and external factors.

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Eva Smorodina

@EvaSmorodina

4 months

AF3 can predict biomolecules with a stable secondary and tertiary structure that relies on evolutionary information and is relatively independent of external factors.

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Eva Smorodina

@EvaSmorodina

1 year

Exciting news 🎊 I'll be joining the EPSRC SABS R3 CDT program at @mplsoxford @UniofOxford in October. This opportunity allows me to explore sustainable biomedical science and responsible research practices 🎓

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Eva Smorodina

@EvaSmorodina

2 years

My first first-author paper is out in #QRBDiscovery @Biophysics_CUP ! "Comparing 2 crystal structures and 12 AlphaFold2-predicted human membrane glucose transporters and their water-soluble QTY variants"

Comparing 2 crystal structures and 12 AlphaFold2-predicted human membrane glucose transporters and...

Comparing 2 crystal structures and 12 AlphaFold2-predicted human membrane glucose transporters and their water-soluble glutamine, threonine and tyrosine variants - Volume 3

www.cambridge.org

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Eva Smorodina

@EvaSmorodina

10 months

@ZhongingAlong @RDasLab Many thanks to @GabriCorso , @ginaelnesr , @sokrypton , @proteinrosh , @HWaymentSteele , and @ZhongingAlong for organizing @workshopmlsb !

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Eva Smorodina

@EvaSmorodina

8 months

Happy Valentine's Day!

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Eva Smorodina

@EvaSmorodina

4 years

Many thanks to Darren Gowers from @molecmodels for working on the A17 antibody 3D model. The model has detachable chains and the DEP molecule. It's awesome and amazing!

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Eva Smorodina

@EvaSmorodina

1 year

Thrilled to be part of Antibody Engineering & Therapeutics Digital Week! Register here: #antibodydiscovery #antibodytherapeutics #antibodies #therapeutics

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Eva Smorodina

@EvaSmorodina

10 months

Will be attending @workshopmlsb and @genbio_workshop today and tomorrow. Let me know if you're around and would like to meet! #NeurIPS2023 @NeurIPSConf

Eva Smorodina

@EvaSmorodina

10 months

Heading to @NeurIPSConf @workshopmlsb next week! Feel free to DM if you'd like to meet there in person. Looking forward to this exciting event!

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Eva Smorodina

@EvaSmorodina

10 months

Heading to @NeurIPSConf @workshopmlsb next week! Feel free to DM if you'd like to meet there in person. Looking forward to this exciting event!

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Eva Smorodina

@EvaSmorodina

1 year

@victorgreiff @HabibBashour @pandaisikit @sokrypton

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Eva Smorodina

@EvaSmorodina

3 years

Excellently defended my term paper yesterday. This is the first or the second time I've liked my performance myself. Thanks for Alexander Tyshkovsky's public speaking course

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Eva Smorodina

@EvaSmorodina

4 months

More details you can find here:

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Eva Smorodina

@EvaSmorodina

4 months

This robot is adorable!

Kathy Y. Wei, Ph.D.

@KathyYWei1

4 months

"Discovering new protein functions requires the ability to describe the function of a protein beyond assigning it to a preexisting class" - and now we can with ProtNLM

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Eva Smorodina

@EvaSmorodina

4 months

Please take into account that this is not a proper research paper and not a thorough benchmarking, so the conclusions won't hold in 100% of cases. However, I believe such observations are worth keeping in mind while conducting your own AF3 runs to have some a priori expectations.

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Eva Smorodina

@EvaSmorodina

2 years

Congratulations and thanks for the collaboration!

Alexander Imani Cowen-Rivers.

@ImanisMind

2 years

Very happy to share “AntBO: Towards Real-World Automated Antibody Design using Combinatorial Bayesian Optimisation” was accepted at @CellRepMethods TL;DR improved ML method for sample efficient CDR design. Paper - Code - /1

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Eva Smorodina

@EvaSmorodina

1 year

Many thanks to my colleagues, friends, and supervisors, especially @victorgreiff , @HabibBashour , @pandaisikit , and @sokrypton , who have supported and helped me during both good and challenging times ⭐️

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Eva Smorodina

@EvaSmorodina

8 months

Who are you as a chemical element?

Valentine's Day 2024 Doodle - Google Doodles

Learn more about the creation of Valentine's Day 2024 Doodle and discover the story behind the unique artwork.

doodles.google

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Eva Smorodina

@EvaSmorodina

10 months

Besides, it was nice to learn more about CryoDRGN and Ribonanza by @ZhongingAlong and @RDasLab

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Eva Smorodina

@EvaSmorodina

5 months

I'll be in Leiden next week at the Workshop on Free Energy Methods in Drug Design. Let me know if you'd like to meet there!

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Eva Smorodina

@EvaSmorodina

3 months

Virtually at @icmlconf #ICML2024 this week. Happy to chat about AI x bio via Zoom! DM and we'll arrange a call

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Eva Smorodina

@EvaSmorodina

2 months

Norway is among strong innovators (in second place after Belgium) across the EU and the neighboring countries.

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Eva Smorodina

@EvaSmorodina

3 years

"Antibody Developability" @WOMBO

seven ex machina

@toomanyspectra

3 years

“Galactic Archaeology With Metal-Poor Stars”

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Eva Smorodina

@EvaSmorodina

2 years

Super useful!

Ajasja 💻🧬🔬

@AjasjaLjubetic

2 years

More interactive applets in the pipeline: an interactive loop picker -- visualization can really help build intuition of future protein design engineers🧑‍🔬.

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Eva Smorodina

@EvaSmorodina

4 months

@AjasjaLjubetic It's not clear which exact structures are in the training dataset. Based on the information provided in the AF3 supplementary, they used a time split. But in this case, structures from the train set still failed to be predicted accurately by AF3 (e.g., 2MXU beta-amyloid fibril)

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Eva Smorodina

@EvaSmorodina

11 months

@amelie_iska I'll post a link soon

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Eva Smorodina

@EvaSmorodina

1 year

After the initial training year, I'll begin a DPhil project focusing on protein design under Professor Yujia Qing supervision. I'm grateful for this amazing opportunity and look forward to the journey ahead 👩‍💻

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Eva Smorodina

@EvaSmorodina

3 years

So true 😅

Andrew Bowman

@bowchro

3 years

When you need a coffee, but fear a @GoogleColab session timeout. #AlphaFold

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Eva Smorodina

@EvaSmorodina

8 months

I'm curious how many early-career scientists (MSc/PhD/PostDoc) in Norway are interested in bio-related entrepreneurship. Do you have a general appeal, do you want to learn more, or maybe you are already developing your idea and launching a startup? @UiO_Doc @UniOslo @UiO_LifeSci

General interest

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Want to be involved

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Eva Smorodina

@EvaSmorodina

11 months

@allyzbo @ProfSyK @fjduarteg @duarte_group Congratulations ✨️

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Eva Smorodina

@EvaSmorodina

4 months

@labriataphd @GoogleDeepMind Nice post, thanks for sharing! Here is my overview of the strong, weak, and questionable sides of AF3:

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Eva Smorodina

@EvaSmorodina

3 years

@H__Spinner Python, RDKit, Biopython, GROMACS, Rosetta, AlphaFold, ABodyBuilder, PyMol

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Eva Smorodina

@EvaSmorodina

11 months

@LeoChan213 @HabibBashour @pariset_matteo @Jahn_Zhong Thank you! For this post's cover image, we used Bing Image Creator. Antibody structures were visualized in PyMOL. We plotted the results using R and organized these plots in Adobe Illustrator. The graphical abstract was created in Biorender

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Eva Smorodina

@EvaSmorodina

2 months

Many thanks to @HabibBashour , @Jahn_Zhong , @pariset_matteo , @victorgreiff , and all other co-authors for the collaborative work on this study!

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Eva Smorodina

@EvaSmorodina

4 months

@HaseebEden Only a limited amount from a list of available ligands

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Eva Smorodina

@EvaSmorodina

10 months

@ginaelnesr @workshopmlsb @genbio_workshop I'm also at MLSB. Would be happy to meet!

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Eva Smorodina

@EvaSmorodina

8 months

@CagiadaMatteo @UCPH_Research @novonordiskfond Congratulations!

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Eva Smorodina

@EvaSmorodina

4 months

@DuckyM2 You can find PTMs if you click on the three dots near the entered sequence on the AF3 website. Then, you can select from the list which type of modification to add to which residue

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Eva Smorodina

@EvaSmorodina

4 months

@DaveJuergens Congratulations!

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Eva Smorodina

@EvaSmorodina

10 months

@genbio_workshop @genbio_workshop

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Eva Smorodina

@EvaSmorodina

10 months

@BasileWicky @ETH_BSSE Congratulations 🎊 🎉

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Eva Smorodina

@EvaSmorodina

11 months

@Gupta_Calling With

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Eva Smorodina

@EvaSmorodina

1 year

@sokrypton @MITBiology Congratulations 🎊

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Eva Smorodina

@EvaSmorodina

10 months

@tommy_da_cat @NeurIPSConf @workshopmlsb I'm at NeurIPS today and tomorrow

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Eva Smorodina

@EvaSmorodina

2 years

@Ahmed_7amada83 @ACSChemRev PyMOL+BioRender

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Eva Smorodina

@EvaSmorodina

4 months

@DuckyM2 I've heard about MODOMICS and NAMDB. I haven't checked them myself, but you can take a look

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Eva Smorodina

@EvaSmorodina

1 year

Lucky to have received an invite code for Bluesky! Fun fact: the platform was founded on the same day as my birthday. Feel free to follow me there for updates in structural bioinformatics and protein design! @evasmorodina .bsky.social

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Eva Smorodina

@EvaSmorodina

4 months

@labriataphd @thesteinegger @GoogleDeepMind It works, thank you very much!

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