BioExcel CoE
@bioexcelcoe.bsky.social
📤 350
📥 133
📝 72
Centre of Excellence for Computational Biomolecular Research
pinned post!
Save the dates! The 3rd BioExcel Conference on Advances in Biomolecular Simulations is happening: 🗓️ 27-30 September 2026 🌐 Brno, Czech Republic ℹ️
bioexcel.eu/hzr0
Registration opens: 19 January 2026
#moleculardynamics
#freeenergy
#drugdesign
#ai
#conference
about 7 hours ago
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Save the dates! The 3rd BioExcel Conference on Advances in Biomolecular Simulations is happening: 🗓️ 27-30 September 2026 🌐 Brno, Czech Republic ℹ️
bioexcel.eu/hzr0
Registration opens: 19 January 2026
#moleculardynamics
#freeenergy
#drugdesign
#ai
#conference
about 7 hours ago
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📢 Our Ambassador Program Adriatic Edition workshop is open for registration ➡️
bioexcel.eu/3c00
Lectures and hands-on tutorials covering
#BioBB
#HADDOCK
and
#PMX
🗓️ 11-12 February 2026 🌍 Ljubljana, Slovenia In collaboration with
@euroccslovakia.bsky.social
EuroCC Italy EuroCC Croatia
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BioExcel / EuroCC workshop in Slovenia
Registration for this event is open Our fourth Ambassador Program workshop is jointly organised and supported by our colleagues at the National Competence Centres in Slovenia, Croatia and Italy. The ...
https://bioexcel.eu/3c00
5 days ago
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🔥Hot off the press! Assessing the performance of the GAFF2/ABCG2 parametrization in protein-ligand relative binding free-energy simulations using non-equilibrium alchemy. Read to learn more ➡️
bit.ly/43aLrA9
@compbiophys.bsky.social
#molecular
#simulation
#drugdiscovery
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Evaluation of the ABCG2 Charge Model in Protein–Ligand Binding Free-Energy Calculations
Accurate binding free energy prediction is vital for drug design, motivating the assessment of new force field models. Here, we evaluate the ABCG2 charge model with nonequilibrium alchemical free-ener...
https://bit.ly/43aLrA9
7 days ago
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reposted by
BioExcel CoE
Alexandre Bonvin
about 1 month ago
INTERNATIONAL SYMPOSIUM ON GRIDS & CLOUDS (ISG) 2026 15-20 March 2026, Academia Sinica, Taipei, Taiwan CALL FOR ABSTRACT There will also be a
#HADDOCK
@bioexcelcoe.bsky.social
workshop in the context of the EU-INDIA GANANA project.
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Last chance to provide your feedback! Our BioExcel 2025 survey is closing tomorrow, 31st October 🎃 Please fill in the survey ➡️bit.ly/3Vi7HE1
12 days ago
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Our BioExcel 2025 survey is closing at the end of October ➡️bit.ly/3Vi7HE1 Please take this opportunity to provide us with your feedback!
25 days ago
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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
about 2 months ago
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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
about 2 months ago
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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
about 2 months ago
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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
about 2 months ago
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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
2 months ago
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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
2 months ago
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🔔 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
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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...
https://bioexcel.eu/ion8
2 months ago
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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
2 months ago
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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
2 months ago
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📢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...
2 months ago
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🤝 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....
3 months ago
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reposted by
BioExcel CoE
BSC-CNS
4 months ago
📢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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👏 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
5 months ago
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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 👋
5 months ago
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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
5 months ago
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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
5 months ago
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Day 2 of the Summer School is about molecular recognition and docking 🤝
@amjjbonvin.bsky.social
introduces
#HADDOCK
to predict interactions between: proteins, nucleic acids, glycans and small molecules For further flexibility and customisation check out HADDOCK3 ➡️bit.ly/4mQLZn7
5 months ago
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First full day of the Summer School on Biomolecular Simulations 2025 in Sardinia 😎 🏖️ It's mostly about
#moleculardynamics
and
#GROMACS
with lectures and hands-on tutorials Check out these useful MD tricks from Prof. Berk Hess👇
5 months ago
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Get inside a bacterial cell with this cool combination of
@cg-martini.bsky.social
and
@viamd.bsky.social
Also check out our recent webinars on each: 🎬 Whole cell simulation with Martini ▶️
youtu.be/fvFaPgSoM90
🎬 Visual analysis of
#moleculardynamics
with VIAMD ▶️
youtu.be/wVENzcx0XmQ
add a skeleton here at some point
5 months ago
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Registration for the Martini workshop, 11-15 August 2025 in Groningen, is now open! Learn from the cocktail masters themselves how to prepare your optimal Martini simulations, making use of the latest tools. Info and application:
cgmartini.nl
Deadline: 15 June
add a skeleton here at some point
5 months ago
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Read about the recent
#compchem
Spring School held
@csc.fi
and 🔑 access the training materials ➡️bioexcel.eu/rj58 ✅ Classical
#moleculardynamics
✅ Electronic structure theory ✅
#machinelearning
in chemistry ✅ Enhanced sampling methods
#quantumchemistry
#AI
6 months ago
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Our webinar series will restart in September 2025 following a break during the summer months ☀️⛱️ 📽️ You can access the recordings of all our previous webinars via our YouTube channel ▶️
bit.ly/3H8FZW7
#molecularmodeling
#molecularsimulations
#research
#compchem
6 months ago
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Join us today 13th May at 15:00 CET for our last webinar before the summer break 😎 "MiMiC: A high-performance framework for multiscale molecular dynamics simulations" Registration ➡️
bioexcel.eu/l4rd
#moleculardynamics
#qmmm
#compchem
6 months ago
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A great opportunity to work with the GROMACS development team in Sweden on enhanced sampling in molecular dynamics🔝🖥️🇸🇪 ℹ️ More information:
bioexcel.eu/u583
🗓️ Application deadline: 2 June 2025
#jobs
#moleculardynamics
6 months ago
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reposted by
BioExcel CoE
Alexandre Bonvin
6 months ago
The manuscript describing the new modular version of HADDOCK is finally available as a preprint! The result of a team work over several years, supported by
@bioexcelcoe.bsky.social
@bijvoet-centre.bsky.social
@esciencecenter.bsky.social
-
www.biorxiv.org/content/10.1...
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Our webinar on "MiMiC: A high-performance framework for multiscale molecular dynamics simulations" is next week on Tuesday 13 May at 15:00 CET Don't forget to register ➡️
bioexcel.eu/l4rd
#moleculardynamics
#qmmm
#compchem
6 months ago
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Last day of this year's Computational Chemistry Spring School held @CSCfi ✅Classic
#moleculardynamics
✅Electronic structure theory ✅#AI in chemistry ✅Hands-on tutorials running on supercomputer GPUs ✅Poster session & networking 🌍24 participants / 8 countries
#compchem
7 months ago
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Join us for our next webinar where Andrej Antalík will introduce the MiMiC framework for multiscale modeling in computational chemistry 🗓️ 13 May 2025, 15:00 CET ✍️ Sign up:
bioexcel.eu/l4rd
#moleculardynamics
#qmmm
#compchem
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Webinar: MiMiC: A high-performance framework for multiscale molecular dynamics simulations (2025-5-13)
Date: 13 May 2025 Time: 15:00 CEST Registration Abstract These days, computational chemists can choose from a wide variety of software packages, each with its own unique features and strengths. Man...
https://bioexcel.eu/l4rd
7 months ago
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Registration for our hybrid workshop closes on 15 April 2025 ‼️ Note the registration requirements before submitting your application ➡️
bioexcel.eu/sl42
#GROMACS
#HADDOCK
#PMX
#software
@eurocc.bsky.social
@euroccbg.bsky.social
7 months ago
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🔜 Join us tomorrow at 15:00 CET (UTC+1) to hear about "Modelling antibodies in the post-Alphafold era: where are we now?" Registration is still open ➡️
bit.ly/4bYUozP
#webinar
#antibody
#AlphaFold
#proteindesign
#compchem
7 months ago
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Our webinar "Modelling antibodies in the post-Alphafold era: where are we now?" is next week on Tuesday 8 April at 15:00 CET Don't forget to register ➡️
bit.ly/4bYUozP
#antibody
#HADDOCK
#AlphaFold
#proteindesign
#compchem
@amjjbonvin.bsky.social
7 months ago
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Interested in an entry-level, hands-on workshop on
#GROMACS
,
#HADDOCK
and
#PMX
software? Look no further than our Ambassador Program event: 🗓️ 21-22 May 2025 🌍 Sofia, Bulgaria & online Info ➡️
bioexcel.eu/sl42
➕EuroCCs Bulgaria, Montenegro, North Macedonia, Romania, Serbia
@euroccbg.bsky.social
8 months ago
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Interested in
#antibody
modelling? Marco Giulini will discuss the current state of antibody modelling in the post-AlphaFold era in our next webinar: 🗓️ 8 April 2025 (15:00 CET) ✍️
bit.ly/4bYUozP
#HADDOCK
#AlphaFold
#proteindesign
#compchem
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Webinar: Modelling antibodies in the post-Alphafold era: where are we now? (2025-4-8)
Date: 8 April 2025 Time: 15:00 CET Registration Abstract Antibodies are specialized proteins used by the immune system to eliminate unrecognized, potentially harmful molecules (antigens). Their abili...
https://bit.ly/4bYUozP
8 months ago
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Our webinar on simulating whole cells is next week Registration link below 👇
add a skeleton here at some point
8 months ago
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Our webinar on "Restoring protein Glycosylation with GlycoShape" is next week on Tuesday 11 March at 15:00 CET Don't forget to register ➡️
bit.ly/41l8PKI
#glycan
#3dstructure
#database
8 months ago
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reposted by
BioExcel CoE
Alexandre Bonvin
8 months ago
Our preprint on using Alfaflow to model antibody H3 loops and demonstrating improved modelling performance of their complexes with HADDDOCK3 is now in
@biorxivpreprint.bsky.social
- Work by Marco Giulini and Xiaoting Xu - supported by
@bioexcelcoe.bsky.social
-
www.biorxiv.org/content/10.1...
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Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles
Motivation Gaining structural insights into antibody-antigen complexes is crucial for understanding antigen recognition mechanisms and advancing therapeutic antibody design. However, accurate predicti...
https://www.biorxiv.org/content/10.1101/2025.02.24.639865v1
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We are 2 weeks away from our webinar on simulating whole cells with the Martini force field 🗓️ 18 March 2025, 15:00 CET ✍️ Sign up:
bit.ly/3QxQWSC
@CG_Martini
8 months ago
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Hurry! Tomorrow (4 March at 15:00 CET) is our webinar on "Cryo-EM structure refinement with density-guided simulations in
#GROMACS
" Register here ➡️
bit.ly/41b6L7W
#webinar
#cryoEM
#moleculardynamics
8 months ago
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Our webinar on "Cryo-EM structure refinement with density-guided simulations in
#GROMACS
" is next week on Tuesday 4 March at 15:00 CET Don't forget to register ➡️
bit.ly/41b6L7W
#webinar
#cryoEM
#moleculardynamics
9 months ago
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☝️Don't forget to register for our
#webinar
by Elisa Fadda on "Restoring protein Glycosylation with Glycoshape" 🗓️ 11 March 2025, 15:00 CET Registration ➡️
bit.ly/41l8PKI
#glycan
#3dstructure
#database
9 months ago
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The ability to simulate whole cells will take biological research to a new level 🦠🔬📈 Join us on 18 March 2025, 15:00 CET to hear Siewert-Jan Marrink present progress on simulating whole cells with the Martini force field Registration ➡️bit.ly/3QxQWSC
@cg-martini.bsky.social
9 months ago
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Our webinar on Cryo-EM structure refinement with density guided simulations in GROMACS is less than a couple of weeks away Register here ➡️
bit.ly/41b6L7W
add a skeleton here at some point
9 months ago
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Join us for our upcoming webinar where Elisa Fadda will talk about the importance of incorporating glycosylation into your structural studies "Restoring protein Glycosylation with Glycoshape" 🗓️ 11 March 2025, 15:00 CET Registration & further info ➡️
bit.ly/41l8PKI
9 months ago
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Our webinar on new features and performance improvements in GROMACS 2025 is next week on Tuesday 18 February at 15:00 CET Don't forget to register ➡️
bit.ly/40Ebbme
#webinar
#moleculardynamics
#GROMACS
9 months ago
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