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BioExcel CoE @bioexcelcoe.bsky.social · 15d

Last chance to register ❗️

Our special edition webinar featuring talks on #topoisomerase inhibition, transmembrane #signalling and #membrane multilamellarity is this afternoon at 15:00 CEST

Register here ➡️bioexcel.eu/ion8

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BioExcel CoE @bioexcelcoe.bsky.social · 21d

Happening next week!

Our 23-September, special edition webinar will feature talks on topoisomerase inhibition, transmembrane signalling and membrane multilamellarity

Register here ➡️bioexcel.eu/ion8

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BioExcel CoE @bioexcelcoe.bsky.social · 26d

5️⃣ Featuring the fifth of our showcase projects

Our automated pipeline, built on BioBBs, uses #AlphaFold, MD simulations, and virtual screening to output a list of ligand poses ➡️ bioexcel.eu/1c1j

#DrugDiscovery #Workflows #CADD #VirtualScreening

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BioExcel CoE @bioexcelcoe.bsky.social · 26d

4️⃣ Featuring the fourth of our showcase projects

Upgrading GROMACS to handle billion-atom systems and enhancing I/O performance and precision, making the first-ever whole-cell simulation possible ➡️ bioexcel.eu/uw67

#MolecularDynamics #GROMACS #ComputationalBiology

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BioExcel CoE @bioexcelcoe.bsky.social · 27d

3️⃣ Featuring the third of our showcase projects

We are tackling the tough-to-predict H3 antibody/nanobody loop using AlphaFlow and hierarchical clustering to create more accurate models ➡️bioexcel.eu/56jw

#Antibodies #AlphaFlow #DrugDiscovery

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BioExcel CoE @bioexcelcoe.bsky.social · 28d

2⃣ Featuring the second of our showcase projects

Through a combination of AlphaFold2 and other tools we are bypassing the limits of traditional MD simulations ➡️ bioexcel.eu/dvy3

#Proteins #MolecularDynamics #GROMACS #AlphaFold2

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BioExcel CoE @bioexcelcoe.bsky.social · 29d

🔔 Don't forget to register for our special edition webinar on 23 September where we will have 3 interesting talks by our BioExcel Summer School 2025 poster prize winners:

Find out more and register here ➡️ bioexcel.eu/ion8

Webinar Special Edition: Summer School 2025 poster prize winners (2025-09-23)

Date: 23 September 2025 Time: 15:00 CET Registration This special edition of the BioExcel webinar series features student speakers who were awarded poster prizes at the BioExcel Summer School 2025. R...

bioexcel.eu

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BioExcel CoE @bioexcelcoe.bsky.social · 29d

1️⃣ Featuring the first of our showcase projects

We use an autoencoder to capture and quantify dynamic differences between protein conformational states ➡️ bioexcel.eu/wv4a

#MolecularDynamics #MachineLearning

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BioExcel CoE @bioexcelcoe.bsky.social · Sep 3

From support and training to which features we should develop in our core software, your views are valuable to us 💎

Our annual survey gives you the opportunity to provide us with all-round feedback

Please fill in the BioExcel 2025 survey ➡️bit.ly/3Vi7HE1

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BioExcel CoE @bioexcelcoe.bsky.social · Sep 2

Zuzana Janáčková is studying for her Ph.D. at the Institute of Organic Chemistry and Biochemistry in Prague, Czech Republic

She will talk about "Oligoarginine peptides bind preferentially to concave phospholipid membranes and induce membrane multilamellarity"

BioExcel CoE @bioexcelcoe.bsky.social · Sep 2

Gesa Freimann is studying for her Ph.D. at the Max Planck Institute for Biology in Tübingen, Germany

She will talk about "Molecular Dynamics Simulations of Af1503 – A Model Protein for Transmembrane Signaling"

@gfreimann.bsky.social

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BioExcel CoE @bioexcelcoe.bsky.social · Sep 2

Jan van Elteren is studying for his Ph.D. at the National Institute of Chemistry and the Faculty of Pharmacy in Ljubljana, Slovenia

He will talk about "Investigating catalytic inhibition of full-length topoisomerase IIA through all-atom molecular simulations"

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BioExcel CoE @bioexcelcoe.bsky.social · Sep 2

📢Our next webinar is a special edition featuring the BioExcel Summer School 2025 poster prize winners

🗓️ Join us on 23 September at 15:00 CET
✍️ Registration and further information ➡️bioexcel.eu/ion8

Find out more about our speakers and their research...

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BioExcel CoE @bioexcelcoe.bsky.social · Aug 6

🤝 Our collaboration with other leading EU #HPC Centres of Excellence has resulted a white paper providing guidance and best practices for CoEs aiming to build their #innovation and #commercialisation capabilities

Read more: bioexcel.eu/k7b9
DOI: dx.doi.org/10.13140/RG....

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Reposted by BioExcel CoE

BSC-CNS @bsc-cns.bsky.social · Jul 4

📢Vacancy: BSC is looking for a Junior Research Engineer Biomolecular Simulations (MDDB/BioExcel)

➡www.bsc.es/ZvN

#job #trabajo #feina @bioexcelcoe.bsky.social

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 16

👏 Congratulations to the Summer School 2025 poster prize winners!

🏆 Zuzana Janáčková
🏆 Jan van Elteren
🏆 Gesa Laura Freimann

Join us for a special edition webinar where they will present their work

🗓️ 23 September 2025, 15:00 CET

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 13

Today was the last day of our Summer School on Biomolecular Simulations 2025 ☀ 🏖

Finishing off with an introduction to QM/MM by Emiliano Ippoliti and a 'careers session' for all participants

Thank you to everyone for a great event 👋

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 12

During the afternoon session we were joined online by Sergey Ovchinnikov who gave some invaluable insights into #alphafold

Sergey talked about AlphaFold3 and its limitations. If you are looking for alternatives, check out ColabFold ➡ bit.ly/3KQEHOe

@sokrypton.org

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 12

As more scientific journals are starting to require reproducibility before publication #BioBB can become invaluable

Check out our #webinar on BioBB and #FAIR workflows ➡️ bit.ly/3xXBcCm

Webinar: Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows (2024-05-28)

View slides on Zenodo Abstract Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomole...

bit.ly

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 12

The tutorial uses #GROMACS as the simulation engine. Find this and other #workflow examples here ➡ bit.ly/3xzZJ0q

#BioBB enables automated system preparation, simulation and analysis, making your workflows and environment reproducible and #FAIR

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 12

Day 4 of the Summer School 2025 was about workflows and protein structure prediction

Adam Hospital introduced BioExcel Building Blocks #BioBB and followed up with a hands-on #tutorial on how to perform protein-ligand complex #moleculardynamics in Jupyter notebooks using BioBB

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 11

Sudarshan Behera gave an intro to free energy calculations followed by a #tutorial on using #pmx and #GROMACS to set up a ligand-binding relative free energy calculation study

Access the tutorial ➡ bit.ly/45Bcp3V and a #webinar on the topic ➡ bit.ly/3XjSJxf 📹

@sudars.bsky.social

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 11

This was illustrated during the hands-on session on calculating the potential of mean force (PMF) along a reaction coordinate using the AWH method in #GROMACS

Find the #tutorial here ➡ bit.ly/4c8xeWG and our #webinar on its application ➡ bit.ly/3xqERbY 📽️

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 11

Day 3 of the Summer School is about enhanced sampling and free energy calculations⚡️

Berk Hess introduced the AWH method implemented in #GROMACS and illustrated its application to alchemical transformations where the main challenge is to define a good reaction coordinate

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BioExcel CoE @bioexcelcoe.bsky.social · Jun 10

An engaging tutorial by Attilio, Giuliano Malloci and Mohd Athar enabled participants to test the #EDESmethod for enhanced sampling ➡ bit.ly/45Rdp3h

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