PRACE Autumn School: Fundamentals of Biomolecular Simulations and Virtual Drug Development

Europe/Brussels
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Description

 

We are pleased to invite you to join HPC Autumn School 2021: „Fundamentals of Biomolecular Modelling and Simulations for Applied Research and Virtual Drug Development“.  The school is organised by BioExcel Centre of ExcellenceSTFC Daresbury LaboratoryNCSA Bulgaria, and Sofia University and in partnership with AstraZeneca and NostrumBiodiscovery.

The week-long training event will provide an introduction to the fundamentals of modern methods for biomolecular simulations - molecular dynamics (MD), 3D QSAR, integrative modelling, free energy and hybrid-QM/MM calculations. Widely used software applications (GROMACS, HADDOCK, PMX, ChemShell) will be presented, and their usage on HPC facilities demonstrated. 

The school program targets applied scientists, who have little experience with computational methodologies and High-Performance Computing (HPC). It will be suitable for junior researchers (post-graduates and post-docs) with a background in natural sciences and, in particular, pharmacy, biochemistry and biophysics. Participants from Central and Eastern Europe are especially welcome.

Participation is free.

Key takeaways from the training:

  • What is High-Performance Computing (HPC)? How is it different, and why is it useful? Experience running simulations on a supercomputer. 
  • How do we model proteins, DNA, lipids, cells and biomolecular systems? What methods and techniques are used for simulations, and how do we interpret the results?
  • What are the popular software applications in the field and how can we use them? 
  • Success stories:  How do we screen for drugs? How do we study biomolecular phenomena? How do we do all of that in days instead of months? Learn from leading scientists from academia and pharma companies.

 

Registration deadline: September 12, 2021

For any further information, please feel free to contact us.

https://www.ncsa.bg/ncsa-training 

 

Surveys
Survey for PRACE Autumn School Fundamentals of Biomolecular Simulations and Virtual Drug Development
    • 09:30 09:50
      HPC for Applied Research 20m

      Join online
      All indicated times are in the Central European Summer Time (CEST) zone (GMT +2)

    • 09:50 10:00
      Opening 10m
      Speaker: Prof. Anela Ivanova (Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria)
    • 10:00 10:50
      Lecture 50m

      • Drug Design: Past, Present and Future

      Speaker: Prof. Irini Doychinova (Medical University, Sofia, Bulgaria)
    • 10:50 11:00
      Lecture 10m

      • BioExcel Centre of Excellence – Advanced applications and services for computational biomolecular research

      Speaker: Dr Rossen Apostolov (KTH Royal Institute of Technology, Sweden)
    • 11:00 11:30
      Break 30m
    • 11:30 12:30
      Lecture 1h

      • Parallelisation paradigms: introduction to methodologies for parallelisation, application of MPI and ОpenMP

      Speaker: Dr Valentin Pavlov (Rila Solutions)
    • 12:30 14:00
      Lunch break 1h 30m
    • 14:00 15:30
      Practical session 1 1h 30m

      • Training (demonstration)

      Speaker: Prof. Emanouil Atanassov (IICT-BAS, Bulgaria)
    • 15:30 16:00
      Break 30m
    • 16:00 16:30
      Practical session 2 30m

      • Discoverer EuroHPC supercomputer

      Speaker: Prof. Ivan Dimov (Member of EuroHPC Governing Board)
    • 09:00 09:30
      Biomolecular Simulations with Molecular Dynamics 30m

      Join online
      All indicated times are in the Central European Summer Time (CEST) zone (GMT +2)

    • 09:30 10:30
      Lecture 1h

      • Basics of Molecular Dynamics

      Speaker: Prof. Anela Ivanova (Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria)
    • 10:30 11:00
      Break 30m
    • 11:00 12:00
      Lecture 1h

      • Introduction to Molecular Dynamics simulations with GROMACS

      Speaker: Prof. Peicho Petkov (Faculty of Physics, Sofia University, Bulgaria)
    • 12:00 13:30
      Lunch break 1h 30m
    • 13:30 15:00
      Practical session 1h 30m

      • Demonstrations on how to prepare and run an MD simulation with GROMACS on a supercomputer

      Prof. Peicho Petkov, Faculty of Physics, Sofia University / Stoyan Iliev, Faculty of Chemistry and Pharmacy, Sofia University

    • 15:00 15:30
      Break 30m
    • 15:30 16:30
      Practical session 1h

      • Best practices and Q&A session on HPC usage of GROMACS for biomolecular simulations

      Speaker: Prof. Berk Hess (KTH Royal Institute of Technology, Sweden)
    • 09:00 09:30
      Integrative modelling, Docking and Free energy calculations of biomolecular systems 30m

      Join online
      All indicated times are in the Central European Summer Time (CEST) zone (GMT +2)

    • 09:30 10:30
      Lectures 1h

      • Introduction to free energy calculations with PMX

      Speaker: Dr Vytautas Gapsys (Max Planck Institute for Biophysical Chemistry, Germany)
    • 10:30 11:00
      Break 30m
    • 11:00 12:00
      Practical session 1h

      • Demonstrations and hands-on session for working with PMX

      Speaker: Dr Vytautas Gapsys (Max Planck Institute for Biophysical Chemistry, Germany)
    • 12:00 12:30
      Industry talk: AstraZeneca 30m

      • Application of molecular dynamics simulations in the field of drug discovery:

      • brief introduction to drug discovery (aims, challenges);
      • small molecule generation and the need to assess their potency;
      • small molecule application use cases (pocket identification, screening, relative and absolute binding free energy predictions)
      Speaker: Dr Christian Margreitter (AstraZeneca, UK-Sweden)
    • 12:30 14:00
      Lunch break 1h 30m
    • 14:00 15:00
      Lecture 1h

      • Basics of docking for drug design
      • Introduction to HADDOCK

      Speaker: Prof. Alexandre Bonvin (Utrecht University, Netherlands)
    • 15:00 15:30
      Break 30m
    • 15:30 16:30
      Practical session 1h

      • Demonstrations and hands-on session for working with HADDOCK

      Speaker: Prof. Alexandre Bonvin (Utrecht University, Netherlands)
    • 09:00 09:30
      DL_Software and Hybrid-QM/MM approaches in biomolecular sciences via ChemShell 30m

      Join online
      All indicated times are in the Central European Summer Time (CEST) zone (GMT +2)

    • 09:30 10:00
      Lecture 30m

      • Introduction to Daresbury Laboratory Molecular Modelling Suite

      Speaker: Prof. Ilian Todorov (STFC Daresbury Laboratory, UK)
    • 10:00 10:45
      Lecture 45m

      • Introduction to ChemShell

      Speaker: Dr Tom Keal (STFC Daresbury Laboratory, UK)
    • 10:45 11:15
      Break 30m
    • 11:15 12:00
      Demonstration 1 45m

      • First steps with ChemShell

      Dr. Tom Keal, STFC Daresbury Laboratory, UK; Dr. You Lu, STFC Daresbury Laboratory, UK; Dr. Kakali Sen, STFC Daresbury Laboratory, UK

    • 12:00 13:30
      Lunch break 1h 30m
    • 13:30 14:15
      Lecture 45m

      • Biomolecular modelling with QM/MM

      Speaker: Dr Kakali Sen (STFC Daresbury Laboratory, UK)
    • 14:15 14:30
      Lecture 15m

      • The Py-ChemShell biomolecular workflow

      Speaker: Dr You Lu (STFC Daresbury Laboratory, UK)
    • 14:30 15:00
      Break 30m
    • 15:00 16:30
      Demonstration 2 1h 30m

      • Biomolecular modelling with ChemShell

      Dr. Tom Keal, STFC Daresbury Laboratory, UK; Dr. You Lu, STFC Daresbury Laboratory, UK; Dr. Kakali Sen, STFC Daresbury Laboratory, UK

    • 09:00 09:30
      Success stories and showcases of using HPC for biomolecular and applied research in Central and Eastern Europe 30m

      Join online
      All indicated times are in the Central European Summer Time (CEST) zone (GMT +2)

    • 09:30 10:00
      Lecture 30m

      • Different approaches for finding ligands inhibiting the NSP10/NSP16 complex of the SARS-CoV-2

      Assoc. Prof. Miroslav Rangelov, Institutes of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciencеs; Dr Nadezhda Todorova, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences; Prof. Dr. José Antonio Encinar, Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDIBE), Spain; Prof. Stoyan Markov, National Center for Supercomputing Applications, Bulgaria

      Speaker: Dr Nadezhda Todorova (Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences)
    • 10:00 10:30
      Lecture 30m

      • In silico study of the anti-inflammatory action of heparin within the Covid-19 context

      Prof. Nevena Ilieva, Institute of Information and Communication Technologies, Bulgarian Academy of Sciences; Assoc. Prof. Peicho Petkov, Faculty of Physics, Sofia University, Bulgaria; Assoc. Prof. Miroslav Rangelov, Institutes of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences; Dr Elena Lilkova, Institute of Information and Communication Technologies, Bulgarian Academy of Sciences; Dr Nadezhda Todorova, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences; Prof. Leandar Litov, Faculty of Physics, Sofia University, Bulgaria

      Speaker: Prof. Nevena Ilieva ( Institute of Information and Communication Technologies, Bulgarian Academy of Sciences)
    • 10:30 11:00
      Break 30m
    • 11:00 11:30
      Lecture 30m

      • Beyond in silico simulations: A case study on acetylcholinesterase inhibitors

      Dr Mariyana Atanasova, Faculty of Pharmacy, Medical University, Bulgaria; Prof. Georgi Stavrakov, Faculty of Pharmacy, Medical University, Bulgaria; Irena Philipova, Faculty of Pharmacy, Medical University, Bulgaria; Dr Dimitrina Zheleva, Faculty of Pharmacy, Medical University, Bulgaria; Prof. Rumyana Simeonova, Faculty of Pharmacy, Medical University, Bulgaria; Prof. Spiro Konstantinov, Faculty of Pharmacy, Medical University, Bulgaria; Prof. Ivan Dimitrov, Faculty of Pharmacy, Medical University, Bulgaria; Prof. Irini Doytchinova, Faculty of Pharmacy, Medical University, Bulgaria

      Speaker: Dr Mariyana Atanasova (Medical University, Sofia, Bulgaria)
    • 11:30 12:00
      Lecture 30m

      • Ligand- and structure-based studies of natural flavonoids from the plant Silybum marianum

      Antonia Diukendjieva, PhD student, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences; Petko Alov, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences; Prof. Ivanka Tsakovska, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences; Prof. Tania Pencheva, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences; Prof. Ilza Pajeva, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences

      Speaker: Prof. Ilza Pajeva (Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences)
    • 12:00 12:30
      Industry talk: NostrumBiodiscovery 30m

      • Could FE calculations with GROMACS be faster? NostrumBiodiscovery's attempt to achieve this goal

      Speaker: Dr Aristarc Surinach (NostrumBiodiscovery, Spain)
    • 12:30 14:00
      Lunch break 1h 30m
    • 14:00 14:30
      Lecture 30m

      • Clustering of doxorubicin and its interaction with bio-polymers (alginates)

      Prof. Petko Petkov, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Nikolay Daskalov, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Prof. Georgi Vayssilov, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria

      Speaker: Prof. Petko Petkov ( Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria)
    • 14:30 15:00
      Lecture 30m

      • Selectivity of binding of vector molecules to the folate receptor-alpha observed by molecular dynamics

      Dr Gergana Gocheva, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Dr Nikoleta Ivanova, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Dr Jasmina Petrova, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Stoyan Iliev, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Ethan N. Schaber, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; PhD Boyana Atanasova, Teva Pharmaceuticals; Prof. Galia Madjarova, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Dr Nina Ilieva, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Prof. Anela Ivanova, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria

      Speaker: Prof. Anela Ivanova (Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria)
    • 15:00 15:30
      Lecture 30m

      • Molecular dynamics simulations of fenofibratå solubilization into bile salt and fatty acids micelles

      Dr Fatmegyul Mustan-Borisova, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Prof. Anela Ivanova, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria; Prof. Slavka Tcholakova, Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria

      Speaker: Dr Fatmegyul Mustan-Borisova (Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria)
    • 15:30 15:45
      Closing remarks 15m
      Speaker: Dr Rossen Apostolov (KTH Royal Institute of Technology, Sweden)