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

20 Sep 2021, 09:30 → 24 Sep 2021, 16:30 Europe/Brussels

Zoom (Zoom)

 

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 Excellence, STFC Daresbury Laboratory, NCSA 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 

 

Monday, 20 September

09:30 → 09:50 HPC for Applied Research

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

09:50 → 10:00 Opening

Speaker: Prof. Anela Ivanova (Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria)

10:00 → 10:50 Lecture

• Drug Design: Past, Present and Future

Speaker: Prof. Irini Doychinova (Medical University, Sofia, Bulgaria)

Drug_Design_Past_Present_and_Future.pdf

10:50 → 11:00 Lecture

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

Speaker: Dr Rossen Apostolov (KTH Royal Institute of Technology, Sweden)

BioExcel_Centre_of_Excellence_Advanced_applications_and_services_for_computational_biomolecular_research.pdf

11:00 → 11:30 Break

11:30 → 12:30 Lecture

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

Speaker: Dr Valentin Pavlov (Rila Solutions)

Parallelisation_paradigms_introduction_to_methodologies_for_parallelisation_application_of_MPI_and_ОpenMP.pdf

12:30 → 14:00 Lunch break

14:00 → 15:30 Practical session 1

• Training (demonstration)

Speaker: Prof. Emanouil Atanassov (IICT-BAS, Bulgaria)

15:30 → 16:00 Break

16:00 → 16:30 Practical session 2

• Discoverer EuroHPC supercomputer

Speaker: Prof. Ivan Dimov (Member of EuroHPC Governing Board)

Discoverer_EuroHPC_supercomputer.pdf

Tuesday, 21 September

09:00 → 09:30 Biomolecular Simulations with Molecular Dynamics

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

09:30 → 10:30 Lecture

• Basics of Molecular Dynamics

Speaker: Prof. Anela Ivanova (Faculty of Chemistry and Pharmacy, Sofia University, Bulgaria)

Basics_of_Molecular_Dynamics.pdf

10:30 → 11:00 Break

11:00 → 12:00 Lecture

• Introduction to Molecular Dynamics simulations with GROMACS

Speaker: Prof. Peicho Petkov (Faculty of Physics, Sofia University, Bulgaria)

Introduction_to_Molecular_Dynamics_simulations_with_GROMACS.pdf

12:00 → 13:30 Lunch break

13:30 → 15:00 Practical session

• 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

15:30 → 16:30 Practical session

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

Speaker: Prof. Berk Hess (KTH Royal Institute of Technology, Sweden)

Wednesday, 22 September

09:00 → 09:30 Integrative modelling, Docking and Free energy calculations of biomolecular systems

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

09:30 → 10:30 Lectures

• Introduction to free energy calculations with PMX

Speaker: Dr Vytautas Gapsys (Max Planck Institute for Biophysical Chemistry, Germany)

Introduction_to_free_energy_calculations_with_PMX.pdf

10:30 → 11:00 Break

11:00 → 12:00 Practical session

• 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

• 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)

Application_of_molecular_dynamics_simulations_in_the_field_of_drug_discovery.pdf

12:30 → 14:00 Lunch break

14:00 → 15:00 Lecture

• Basics of docking for drug design
• Introduction to HADDOCK

Speaker: Prof. Alexandre Bonvin (Utrecht University, Netherlands)

Integrative_modeling_of_biomolecular_complexes.pdf

15:00 → 15:30 Break

15:30 → 16:30 Practical session

• Demonstrations and hands-on session for working with HADDOCK

Speaker: Prof. Alexandre Bonvin (Utrecht University, Netherlands)

Thursday, 23 September

09:00 → 09:30 DL_Software and Hybrid-QM/MM approaches in biomolecular sciences via ChemShell

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

09:30 → 10:00 Lecture

• Introduction to Daresbury Laboratory Molecular Modelling Suite

Speaker: Prof. Ilian Todorov (STFC Daresbury Laboratory, UK)

10:00 → 10:45 Lecture

• Introduction to ChemShell

Speaker: Dr Tom Keal (STFC Daresbury Laboratory, UK)

10:45 → 11:15 Break

11:15 → 12:00 Demonstration 1

• 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

13:30 → 14:15 Lecture

• Biomolecular modelling with QM/MM

Speaker: Dr Kakali Sen (STFC Daresbury Laboratory, UK)

14:15 → 14:30 Lecture

• The Py-ChemShell biomolecular workflow

Speaker: Dr You Lu (STFC Daresbury Laboratory, UK)

14:30 → 15:00 Break

15:00 → 16:30 Demonstration 2

• 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

Friday, 24 September

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

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

09:30 → 10:00 Lecture

• 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)

Different_approaches_for_finding_ligands_inhibiting_NSP10NSP16_complex_of_SARS-CoV-2.pdf

10:00 → 10:30 Lecture

• 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)

In_silico_study_of_anti-inflammatory_action_of_heparin_within_Covid-19_context.pdf

10:30 → 11:00 Break

11:00 → 11:30 Lecture

• 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)

Beyond_in_silico_simulations_case_study_on_acetylcholinesterase_inhibitors.pdf

11:30 → 12:00 Lecture

• 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)

Ligand_and_structure-based_studies_of_natural_flavonoids_from_plant_Silybum_marianum.pdf

12:00 → 12:30 Industry talk: NostrumBiodiscovery

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

Speaker: Dr Aristarc Surinach (NostrumBiodiscovery, Spain)

Could_FE_calculations_with_GROMAC_ be_faster_NostrumBiodiscovery's_attempt_to_achieve_this_goal.pdf

12:30 → 14:00 Lunch break

14:00 → 14:30 Lecture

• 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)

Clustering_of_doxorubicin_and_its_interaction_with_bio-polymers_alginates.pdf

14:30 → 15:00 Lecture

• 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)

Selectivity_of_binding_of_vector_molecules_to_folate_receptor_observed_by_molecular_dynamics.pdf

15:00 → 15:30 Lecture

• 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)

Molecular_dynamics_simulations_of_fenofibrata_solubilization_into_bile_salt_and_fatty_acids_micelles.pdf

15:30 → 15:45 Closing remarks

Speaker: Dr Rossen Apostolov (KTH Royal Institute of Technology, Sweden)