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SUMMARY:BioExcel / EuroCC workshop on Biomolecular Simulations: Aegean Edi
 tion
DTSTART;VALUE=DATE-TIME:20261118T074500Z
DTEND;VALUE=DATE-TIME:20261120T124500Z
DTSTAMP;VALUE=DATE-TIME:20260820T000701Z
UID:indico-event-211@events.grnet.gr
DESCRIPTION:\n\nBioExcel / EuroCC workshop on Biomolecular Simulations: Ae
 gean Edition \n\nDate: November 18-20\, 2026\n\nLocation: Biomedical Rese
 arch Foundation of the Academy of Athens (BRFAA)\n\nType of the event:  H
 ybrid (30 on-site + 10 online participants)\n\nPresentation Language: Engl
 ish\n\nAudience: Suitable for  graduate students\, postdocs\, PIs\n\nPart
 icipation criteria: Open application with a selection. 30 applicants will 
 be selected for on-site participation and 10 on-line. Applicants from Gree
 ce and Türkiye will be prioritised for on-site participation. The worksho
 p can only accept participants from EuroHPC Joint Undertaking member insti
 tutions. Remote participants from the Aegean region and other areas outsid
 e Athens will be given priority. \n\nCost: Free of charge\n\nWorkshop Desc
 ription: This three-day workshop covers biomolecular modeling\, simulation
  workflows and integrative structural biology. The event pairs lectures wi
 th hands-on tutorials using Jupyter Notebooks and web portals across three
  methods: GROMACS\, BioBB and HADDOCK. The workshop is co-roganised by  
 BioExcel CoE\, EuroCC@Greece\, the Biomedical Research Foundation of the A
 cademy of Athens and Izmir Biomedicine and Genome Center of the Dokuz Eylu
 l University. \n\n \n\nAgenda breakdown:\n\nModule 1: Introduction to MD 
 & Trajectory Analysis (GROMACS)\n\n\n	\n	Instructors: Alessandra Villa (KC
 SC)\n	\n	\n	Date: 18 November (Lecture & Tutorial)\n	\n\n\nThis module cov
 ers classical force fields\, boundary conditions and numerical integration
  used to simulate macromolecular trajectories.\n\nParticipants will learn 
 to:\n\n\n	\n	Prepare and check an experimental PDB structure.\n	\n	\n	Defi
 ne topologies\, parameterize molecules\, and select force fields.\n	\n	\n	
 Solvate the system and neutralize charges with ions.\n	\n	\n	Run energy mi
 nimization\, along with NVT and NPT equilibration phases.\n	\n	\n	Run prod
 uction MD and analyze trajectories via Root Mean Square Deviation (RMSD)\,
  Root Mean Square Fluctuation (RMSF) and Radius of Gyration (Rg​).\n	\n\
 n\nModule 2: Automated Biomolecular Workflows (BioBB)\n\n\n	\n	Instructor:
  Adam Hospital (IRB Barcelona)\n	\n	\n	Date: 19 November (Lecture & Tutori
 al)\n	\n\n\nThis module introduces the BioExcel Building Blocks (BioBB) Py
 thon library to build automated\, reproducible simulation pipelines that f
 ollow FAIR data principles.\n\nParticipants will learn to:\n\n\n	\n	Use Bi
 oBB modules inside Jupyter Notebooks to link separate simulation steps.\n	
 \n	\n	Automate structure checking\, system preparation\, solvation\, equil
 ibration\, and GROMACS execution blocks.\n	\n	\n	Handle parameter adjustme
 nts programmatically\, track data provenance\, and scale workflows across 
 computing setups.\n	\n\n\nModule 3: Integrative Structural Biology: MD & H
 ADDOCK & Cryo-EM\n\n\n	\n	Instructors: Alexandre Bonvin (Utrecht Universit
 y)\, Panagiotis Kastritis (MLU Halle-Wittenberg)\n	\n	\n	Dates: 19–20 No
 vember (Lectures & Tutorials)\n	\n\n\nThis module covers information-drive
 n docking to model large macromolecular complexes by combining electron mi
 croscopy data with computational prediction in HADDOCK.\n\nParticipants wi
 ll learn to:\n\n\n	\n	Preprocess Data: Crop Cryo-EM density maps and use P
 owerFit 6D cross-correlation searches to locate subunit centroids.\n	\n	\n
 	Restraint-Driven Docking: Convert centroid coordinates into distance rest
 raints in HADDOCK to drive initial rigid-body docking.\n	\n	\n	Refinement 
 & Scoring: Run semi-flexible simulated annealing in explicit solvent\, app
 ly density scoring terms\, and cluster the resulting structural configurat
 ions.\n	\n\n\n \n\nImportant dates:\n\n\n	10 July 2026: Registration open
 s\n	25 September 2026: Registration closes\n	5 October 2026: Notification 
 of selected participants\n	10 October 2026: Deadline for confirmation of a
 ttendance \n\n\nFor any questions regarding the workshop or the applicatio
 n / registration process\, please contact us at: zoe@bioacademy.gr \n\n
  \n\n---\n\n \n\n \n\n\n\nEuroCC 3 has received funding from the Europe
 an High-Performance Computing Joint Undertaking (JU) under Grant Agreement
  No. 101306701. The JU receives support from the European Union‘s Digita
 l Europe Programme and Germany\, Albania\, Austria\, Belgium\, Bosnia and 
 Herzegovina\, Bulgaria\, Croatia\, Cyprus\, Czechia\, Denmark\, Estonia\, 
 Finland\, France\, Greece\,Hungary\, Iceland\, Ireland\, Italy\, Latvia\, 
 Lithuania\, Luxembourg\, Malta\, Montenegro\, the Netherlands\, North Mace
 donia\, Norway\, Poland\, Portugal\, Romania\, Serbia\, Slovakia\, Sloveni
 a\, Spain\, Sweden\, Türkiye\, and Kosovo. \n\nFunded by the European Un
 ion. Views and opinions expressed are however those of the author(s) only 
 and do not necessarily reflect those of the European Union or EuroHPC Join
 t Undertaking. Neither the European Union nor the EuroHPC Joint Undertakin
 g can be held responsible for them. \n\nhttps://events.grnet.gr/event/211
 /
LOCATION:
URL:https://events.grnet.gr/event/211/
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