BioExcel CoE

📢Registration is now open for the "2nd BioExcel Conference on Advances in Biomolecular Simulations" ➡️ bit.ly/3TBqidQ 🗓 20 - 23 October 2024 📍 Brno, Czech Republic The conference will bring together members of the biomolecular research community from industry and academia to explore and discuss the latest trends, updates and challenges in the fields of integrative modelling, free energy and drug design, workflows, automation and data integration. 📩 We strongly encourage you to submit an abstract and give a talk alongside the great line-up of confirmed speakers: Massimiliano Bonomi, John Chodera, Cecilia Clementi, Pilar Cossio, Leonardo De Maria, Elisa Fadda, Frauke Graeter, Gerhard Hummer, Erik Lindahl, Siewert-Jan Marrink, Antonia Mey, Jean-Philip Piquemal The conference is organised by BioExcel CoE in collaboration with Scientifika Rossen Apostolov Alexandre Bonvin Dana Cernoskova Richard Norman

🚨 Don't miss your chance to influence what we do and how we do it! Our annual survey provides an opportunity for users of our software, support and services to let us know what they like and where there is room for improvement 📈 This year we have combined our individual software surveys into one and added some more general questions about training, support and community engagement ➡ bit.ly/3xydJYN #GROMACS #HADDOCK #PMX #BioBB #training #community #moleculardynamics #molecularmodeling #molecularsimulation #compchem #AI

👏 Congratulations to the BioExcel Summer School 2024 poster prize winners! 🏆 Michel Mom; "Understanding Nanopore Sequencing with Molecular Dynamics Simulations" 🏆 Marta Devodier; "Effective Data-Driven Collective Variables for Free Energy Calculations from Metadynamics of Paths: the case of the human Adenosine Receptor type 2A" 🏆 Sachin Shivakumar; "Implemention of Force Matching Algorithm within the Extremely Scalable MiMiC Framework for Multiscale QM/MM Simulations" They will all receive a discount voucher for the second BioExcel Conference on Advances in Biomolecular Simulations being held in Brno, Czech Republic (bit.ly/3TBqidQ); free support from one of our experts to help progress their research; and the opportunity to present their work at our webinar on 27 August 2024. Save the date!

Today was the last day of our Summer School on Biomolecular Simulations 2024 ☀ 🏖 🔸 We finished off with an introduction to QM/MM by Emiliano Ippoliti, a 'careers session' for all participants and a final coffee in beautiful settings 🔸 Thank you to all participants, trainers and organisers for a great event 🔸 We hope everyone had a safe journey back and please stay in touch! #training #community #molecularsimulations #moleculardynamics #MolecularRecognition #EnsembleDocking #Metadynamics #VirtualScreening #QMMM #compchem #AI

Day 4 of the BioExcel Centre of Excellence Summer School on Biomolecular Simulations 2024 ☀ 🏖 was about free energy calculations and we were joined (virtually) by a special guest 🔸Bert de Groot provided an introduction to free energy calculations using #pmx and this was followed by a hands-on #tutorial by Sudarshan Behera on how to use pmx and #GROMACS to set up alchemical free energy calculations for a ligand-binding relative free energy calculation study 🔸 You can access the tutorial ➡ bit.ly/45Bcp3V and a #webinar on the topic ➡ bit.ly/3XjSJxf 🎞 🔸 Did you know that you can compute around 5,000 alchemical protein-ligand binding free energy calculations per day on #HPC systems? Check out this recent benchmarking study ➡ bit.ly/4csStCu ☁ 💻 💊 🔸 During the afternoon session we were joined by Sergey Ovchinnikov who gave participants some invaluable insights into #alphafold and what to look out for when using it 🔸 Sergey talked about the recent release of AlphaFold3 and its limitations. If you are looking for alternatives, check out ColabFold ➡ bit.ly/3KQEHOe 🔹 To end the day, we engaged in some sightseeing, social activities and dinner in the beautiful town of Pula 🚌 🍽 Looking forward to our last day (day 5) of the BioExcel Summer School 2024! #training #community #molecularsimulations #compchem #drugdiscovery #AI

Join us in this workshop about training and upskilling your users? EMBL-EBI Training co-organises it as part of our effort on RItrainPlus and in collaboration with BioExcel CoE.

Day 3 of the BioExcel Centre of Excellence Summer School on Biomolecular Simulations 2024 ☀ 🏖 and the main topic for discussion was Enhanced Sampling and its application 🔸 Erik Lindahl started us off with a reminder to think and design our computational simulations carefully when attempting to test hypotheses and answer scientifically relevant questions. Check out the attached pic to benefit from Erik's wisdom 🦉 🔸 #GROMACS' implementation of various enhanced sampling methods can help support testing by: improving the efficiency of resource usage, sampling specific degrees of freedom and model dynamics on longer timescales, thus capturing slow transitions and conformational changes. 🔸 The hands-on session on calculating the potential of mean force (PMF) along a reaction coordinate using the accelerated weight histogram method (AWH) in GROMACS helped illustrate one of the relevant methodologies. Find the #tutorial here ➡ bit.ly/4c8xeWG and a recent #webinar on its application ➡ bit.ly/3xqERbY 🎞 🔸 Attilio Vittorio Vargiu, our BioExcel Ambassador for Italy, gave an in-depth brainstorming lecture on biomolecular recognition and enhanced sampling methods, covering techniques like Replica Exchange MD, Metadynamics, Accelerated MD, Targeted MD, and more, illustrated with multiple case studies 🔸 An engaging tutorial by Giuliano Malloci and MOHD ATHAR enabled participants to test the #EDESmethod for enhanced sampling ➡ bit.ly/45Rdp3h 🔸 The latest version of the EDES method (gEDS) which is designed to enhance the sampling of bound (holo)-like protein conformations, thereby improving docking performance and accurately predicting substrate-specific binding events for challenging biological targets was presented. Check out the latest publication bit.ly/4cvLNnk 📒🔬 Looking forward to day 4! #training #community #molecularsimulations #moleculardynamics #MolecularRecognition #EnsembleDocking #Metadynamics #VirtualScreening #ProteinConformations

Day 2 of the BioExcel Centre of Excellence Summer School on Biomolecular Simulations 2024 ☀ 🏖 was all about integrative modelling and workflows 🔸 Adam Hospital started proceedings introducing #BioBB and followed up with a hands-on #tutorial on how to perform protein-ligand complex Molecular Dynamics in Jupyter notebooks using BioBB. The tutorial uses #GROMACS as the simulation engine and you can find this and other #workflow examples here ➡ bit.ly/3xzZJ0q 🔸 In addition to automating system preparation, simulation and analysis BioBB enables your workflows, including the environment, to be encapsulated in a container making them reproducible and #FAIR 🔸 🔬 📒 Scientific journals are starting to require reproducibility before publication and this is where BioBB can come to your aid ⛑ Check out the recent #webinar on BioBB and FAIR workflows ➡ bit.ly/3xXBcCm 🔸 During the afternoon session Alexandre Bonvin introduced the various flavours of #HADDOCK which can be used to predict the interactions between a plethora of distinct molecular types; including proteins, nucleic acids, glycans and small molecules 🔸 The new modular version of HADDOCK (HADDOCK3) allows for further flexibility and customisation of tasks and the long-awaited publication on the HADDOCK 2.4 webserver is now freely available ➡ rdcu.be/dK4Hr 🔸 Victor REYS took participants through the HADDOCK3 tutorial for antibody-antigen modeling. This tutorial and other useful learnings including how to carry out antibody-antigen structure prediction from sequence using #alphafold can be found here ➡ bit.ly/4cvJznX Looking forward to day 3! #training #community #molecularsimulations #compchem #AI

Yesterday we kicked-off our Summer School on Biomolecular Simulations 2024 near the beautiful town of Pula, Sardinia ☀ 🏖 🔸 Following the initial formalities around logistics, day 1 started with a lecture and hands-on #tutorial combo on #moleculardynamics by Alessandra Villa 🔸 We are running the "Introduction to Molecular Dynamics" tutorial on interactive Jupyter Notebooks and you can access this through the #GROMACS tutorials page ➡bit.ly/4csBQab 🔸 Laptops and support is being provided by Sardegna Ricerche and we are extremely grateful for this 🔹 Our formal community building activities started in the afternoon, during which participants were given the opportunity to introduce themselves through a series of flash talks 🔹 These were complemented by the poster sessions which gave rise to much interest and discussion. We are looking forward to finding out who our poster prize winners will be later in the week! 🏆 🔹 To further promote discussions and interactions we are running a 'Living Document' on #hedgedoc where participants can ask questions and share information and we are also running a private Summer School 2024 topic on our BioExcel Forum ➡bit.ly/4baB1lb 🔹 Content will be shared with all participants after the school is finished We are looking forward to the rest of the week, which promises to be packed with further learning 📖 excellent science 🔬 and community building 🤝 #training #community #molecularsimulations #compchem

The registration deadline for our workshop on "Upskilling and training users in science and research" is just 2 weeks away on Friday 28 June. Registration is free (travel and accommodation not included) with some travel bursaries available (based on eligibility) See the original post for further information ⬇