Sebastian Kmiecik

researcher, life sciences surfer, professor at the University of Warsaw @UniWarszawski

[Sebastian Kmiecik @sekmi]

we are currently hiring! independent and creative individuals willing to play with protein-protein and protein-peptide puzzles, see https://t.co/xDRJEliJhZ

#bioinformatics #alphafold #peptidedesign #machinelearning #jobs #jobsearch

[NITHIN C @nithin_aneesh]

When does MD improve RNA models?

Study on 61 CASP15 #RNA with #Amber #χOL3 shows when MD refines vs reveals instability, with practical #guidelines. Use #MD 𝗮𝘀 𝗮 #𝗱𝗶𝗮𝗴𝗻𝗼𝘀𝘁𝗶𝗰 𝘁𝗼𝗼𝗹, 𝗻𝗼�� 𝗮 𝘂𝗻𝗶𝘃𝗲𝗿𝘀𝗮𝗹 𝗳𝗶𝘅𝗲𝗿.

Full article at: https://t.co/qbHQXsKCaG

[Sebastian Kmiecik @sekmi]

Our new paper asks a question: does molecular dynamics actually improve RNA models — or just reveal their limits? The answer isn’t simple.

https://t.co/GakNSlihbf

#RNA #MolecularDynamics #ComputationalBiology #StructuralBiology

[Sebastian Kmiecik @sekmi]

@MissAgataStar @m_gorna W regulaminie szkoly dr nauk scislych i przyrodniczych UW jest mozliwosc zwolnienia z posiadania mgr w szczegolnych sytuacjach jakichs osiagniec, i komisja to klepnela. Co ciekawe innej szkole dr UW, miedzydziedzinowej, nie bylo takiej mozliwosci

[Daisuke Kihara @d_kihara]

CASP protein structure competition nears end as NIH grant money runs out | Science | AAAS https://t.co/LUSLD8RiPO

[Sebastian Kmiecik @sekmi]

💡 CABS-flex 3.0 offers 4 flexibility modes:
🔹 Rigid – minimal motion, close to the native structure
🔹 Flexible – loops & unstructured regions can move
🔹 Rigid-pLDDT – adapts flexibility based on AlphaFold confidence
🔹 Unleashed – no restraints, full conformational freedom

What you get after simulation:

🔍 Interactive 3D viewer (Mol*) – explore structure, RMSF, pLDDT, and more
📊 Fluctuation plots – residue-level RMSF with secondary structure overlays
🧩 Contact maps – dynamic, clickable, chain-by-chain
📦 10-model ensemble download (PDB & trajectory)

All structures reconstructed with AI-based cg2all = high-quality atom-level detail.

[Sebastian Kmiecik @sekmi]

Need to assess protein flexibility or model peptide structures? Check out CABS-flex 3.0 — a fast, intuitive web server, now published in Nucleic Acids Research.

🖥️ Free and browser-based:
https://t.co/C3zagys3iQ

#CABSflex #ProteinDynamics #PeptideModeling #StructuralBioinformatics

[Sebastian Kmiecik @sekmi]

Want to see where your protein is flexible?
Upload any @rcsbPDB structure and get nice flexibility visualizations — straight from your browser.

🚀CABS-flex 3.0 is the third generation of our web server for protein flexibility simulation and peptide modeling — now published in @NAR_Open!

🔗https://t.co/wY0T2WPigR
📖https://t.co/C3zagys3iQ

Compatible with structure data from @PDBeurope and AlphaFold DB (@emblebi), developed at @UniWarszawski
#CABSflex #ProteinDynamics #Bioinformatics #StructuralBioinformatics #AlphaFold

[Sebastian Kmiecik @sekmi]

Attempts to force ESMFold for protein-peptide docking and testing AlphaFold3 along the way.
#peptidedocking #esmfold #peptidetherapeutics https://t.co/v1rMngVnB1

[Sebastian Kmiecik @sekmi]

#3ProcentNaNaukę

[Dariusz Jemielniak @JemielniakD]

@sankowski i ja wpadliśmy na pomysł: całe środowisko, razem musi walczyć o #3ProcentNaNaukę. 3% PKB to nasz interes narodowy. @Lukasiewicz_pl @IDEAS_NCBR @PAN_akademia @NCN_PL - to nie są osobne sprawy. RAZEM twórzmy wspólny front w obronie nauki. Pomóżcie, bo faktycznie utonie.

[Biology+AI Daily @BiologyAIDaily]

Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity

1/ Aggrescan4D (A4D) introduces a novel dimension in protein aggregation prediction by incorporating pH into structural analysis, allowing scientists to explore how environmental pH affects protein stability and aggregation propensity.

2/ Building upon the successful Aggrescan3D tool, A4D goes further by integrating dynamic mode simulations and structural flexibility, offering a more realistic and nuanced understanding of protein aggregation.

3/ A4D's pH-dependent analysis is a game-changer, especially for studying biotechnological applications where pH fluctuations impact protein solubility and disease mechanisms like Alzheimer's and Parkinson's.

4/ A4D also supports advanced protein engineering. Users can simulate and propose mutations that enhance solubility without compromising protein structure, paving the way for more effective therapeutic protein design.

5/ The tool has demonstrated superior accuracy in comparison to other state-of-the-art structure-based prediction tools, like CamSol and SolubiS, with an impressive track record in predicting mutation-driven solubility and aggregation changes.

@sekmi @pfdlab @PPMC_UAB @OriolBarcenas
💻Code: https://t.co/CvmNacoa8l
📜Paper: https://t.co/MOwWMb7DvF

[Ventura's Lab @PPMC_UAB]

Excited to share our new paper with @sekmi lab! Dive into the details and possibilities of Aggrescan4D, the latest A3D update featuring pH-dependent #protein #aggregation prediction! Now in Protein Science!
@ProteinSociety
@UABBarcelona
@IBB_UAB
@I3ptT
https://t.co/GpLo9yNnhE

[Marcin Czerwinski @CzerwinsMarcin]

Another important paper from @k_mikolajczyk and
@sekmi: how heterodimerization with β1,4-galactosyltransferases 1 and 5 (B4galt1/5) influences dual acceptor specificity (GP vs GSL) of Gb3/CD77 synthase (human α1,4-galactosyltransferase, A4galt)
https://t.co/WUm6WSRsow
#glycotime

[Molecure @molecure_sa]

We are thrilled to announce the publication of our collaborative work with Prof. Sebastian Kmiecik, featured in Nucleic Acids Research! 🎉

This article confirms our unique expertise in the area of development of new drugs modulating mRNA function 🔬

➡️ https://t.co/3QOpj2Afr7

[Sebastian Kmiecik @sekmi]

The joint effort between @UniWarszawski @ChemistryUW and @molecure_sa

[Sebastian Kmiecik @sekmi]

Our new study compares RNA 3D structure prediction methods, focusing on RNA-small molecule binding sites. AlphaFold 3 shows potential on the level of other ML-based methods despite some accuracy challenges. With @molecure_sa #AlphaFold #RNA #RNAstructure

https://t.co/6Q0oFrxuOB

[Ventura's Lab @PPMC_UAB]

🚀 Excited to publish Aggrescan4D (A4D) in @NAR_Open!!! Building on the popular A3D server, A4D predicts pH-dependent protein aggregation and offers automated mutation protocols to enhance protein solubility. Explore A4D advanced features! #ProteinResearch
https://t.co/JWcIoIJCCd

[czuchnowski @czuchnowskiw]

Z bólem i po długich przemyśleniach piszę o sprawie "spowiedzi" Marcina Kąckiego....
https://t.co/JOALSUeuL2

[Ventura's Lab @PPMC_UAB]

🔬 Studying protein aggregation in S. cerevisiae just got easier! 🍞🍺 Introducing A3DyDB, your go-to resource for pre-computed predictions on yeast protein structural aggregation, with @sekmi. 📊 #ProteinAggregation #YeastResearch #A3DyDB

https://t.co/9HjNXV1ucc