The PRACE Autumn School on the Fundamentals of Biomolecular Modelling and Simulations for Applied Research and Virtual Drug Development
September 20-24, 2021
The school will provide an introduction to the fundamentals of modern approaches employed for modelling and prediction of the behaviour of bioactive systems and functional materials – – molecular dynamics (MD), 3D Quantitative structure-activity relationship (3D QSAR) and QM/MM. We will focus on docking and MD-based free energy calculations and applying Quantum mechanics/Molecular mechanics (QM/MM) methods to study enzymatic reactions.
The capacity of HPC facilities for performing such simulations will be outlined with an emphasis on commonly applied parallelisation techniques in computational science. All lectures and computational methods will be presented in a way accessible to applied scientists who are not specialists in those fields but would like to broaden their research scope. Lectures will be supplemented by demonstrations using GROMACS, HADDOCK and ChemShell - widely used software packages for HPC modelling and simulations. The target audience is junior researchers (post-graduates and post-docs) with a background in natural sciences and in particular, pharmacy, biochemistry and biophysics, working at European academic research institutions and industry. Trainees from Central and Eastern Europe are especially welcome. Participation is free.
The school is a joint initiative of PRACE, the BioExcel Centre of Excellence, STFC Daresbury Laboratory, NCSA Bulgaria, and Sofia University.
The activities will be carried out online using Zoom.
Day 1, September 20: HPC for applied research
• Introduction to PRACE and HPC
• Parallelisation paradigms: introduction to methodologies for parallelisation, application of MPI and ОpenMP
• Training (demonstration) on access to a petascale supercomputer Discoverer located in Sofia, organisation of files and batch scripts, running and tracking jobs, transfer of files
Day 2, September 21: Biomolecular simulations with Molecular Dynamics
• BioExcel – scope and objectives
• Basics of Molecular Dynamics
• Introduction to Molecular Dynamics simulations with GROMACS
• Demonstrations on how to prepare and run an MD simulation with GROMACS on a supercomputer
• Q&A session on advanced usage of GROMACS for biomolecular simulations
Day 3, September 22: Integrative modelling, Docking and Free energy calculations of biomolecular systems
• Basics of docking for drug design
• Introduction to HADDOCK
• Demonstrations and hands-on session for working with HADDOCK
• Introduction to free energy calculations with PMX
• Demonstrations and hands-on session for working with PMX
Day 4, September 23: Hybrid-QM/MM in biomolecular sciences
• Introduction to ChemShell
• Biomolecular modelling with ChemShell
• Examples of ChemShell application for enzymatic reactions
Day 5, September 24: Success stories and showcases of using HPC for biomolecular and applied research in Central and Eastern Europe
• Several (5-6) 30-minutes presentations demonstrating results from scientific studies conducted on HPC facilities
Dr Rossen Apostolov – coordinator, BioExcel Centre of Excellence, KTH, Sweden
Georgi Prangov – assistant, NCSA
Prof. Ilian Todorov – UKRI-STFC Daresbury Laboratory, UK
Stoyan Iliev – Sofia University “St. Kliment Ohridski”, Bulgaria
Petia Petkova – assistant, NCSA
Prof. Dr. Anela Ivanova – coordinator, Sofia University “St. Kliment Ohridski”, Bulgaria
Prof. Irini Doychinova – Medical University Sofia, Bulgaria
Dr Thomas Keal – UKRI-STFC Daresbury Laboratory, UK
Dr Alessandra Villa – BioExcel Centre of Excellence, KTH, Sweden
Dr. Peicho Petkov – NCSA, Bulgaria
Please fill out this form
Deadline for registrations: July 31
For any further information, please feel free to contact us.
Young Researchers Event 2018
Brain models and Computation for Brain Medicine
Bulgarian Academy of Sciences, Sofia, Bulgaria
18 April 2018
This event is open to the entire scientific community but especially targets young researchers. “Young Researchers Event: Brain models and Computation for Brain Medicine” is a Bulgarian Presidency event on Human Brain Project and High Performance Computing, organised with the support of the European Commission. It will take place on 18 April 2018 at the Big Auditorium of the Bulgarian Academy of Sciences.