6ADD workshop/challenge (30.1.-3.2.2023) is focused on using in silico tools and approaches in drug design. We cover both structure-based drug design (molecular docking, molecular dynamics, structural bioinformatics tools) and ligand-based drug design (QSAR, pharmacophores, deep learning) with lectures and on-hand tutorials. Last day you can try your skills on the ligand selection challenge.

Invited lecturers

prof. Thierry Langer (UniVie, Vienna), assoc. prof. Johannes Kirchmair (UniVie, Vienna), dr. Melissa F. Adasme (EMBL-EBI), dr. James Blackshaw (EMBL-EBI), dr. Wim Dehaen (UCT Prague), dr. Maria Matveieva (UCT Prague), dr. Olena Mokshyna (IOCB Prague), dr. Semen Yesylevskyy (IOCB Prague, IOP Kiev)

Lecturers and Organizers

doc. Karel Berka (KFC UPOL), dr. Pavel Polishchuk (IMTM UPOL), Alina Kutlushina (IMTM UPOL), Aleksandra Ivanova (IMTM UPOL), dr. Václav Bazgier (KFC UPOL), Kateřina Storchmannová (KFC UPOL), Dominik Martinát (KFC UPOL), Anna Špačková (UPOL)

Registration

The meeting will be in a hybrid format. Lectures and tutorial files will be available online, but the on-hand tutorials and challenge will be only on-site. 

Registration are now closed.

Attendance of the event is free of charge. The lecture room holds up to 30 seats. Registrations with poster presentations were prioritized.

Posters

Participants can present their own research through an on-site poster session.
Poster abstract registration is now closed.

Poster abstracts are available in a Book of Abstracts.

Venue

Palacky University Olomouc (UPOL)

Faculty of Science

tř. 17. listopadu 12, Olomouc 77900, Czech Republic

room 3.002

Directions to venue - to the Faculty of Science Palacky University Olomouc

Program

A detailed final program is available here:

The meeting starts on Monday at noon and ends on Friday afternoon after the challenge.

Course Materials

The language of the event is English. All course material will be available on this webpage:

  1. Welcome – Karel Berka
  2. Drug_design_intro – Karel Berka
  3. ChEMBL training + ChEMBL Tutorial Handouts – Melissa F. Adasme, James Blackshaw
  4. Structural bioinformatics tools for drug design – Karel Berka
  5. Alphafoldology_- Karel Berka
  6. Molecular similarity and optimization – Wim Dehaen
  7. Fantastic natural_products and where to find them – Olena Mokshyna
  8. Metabolism prediction – Johannes Kirchmair
  9. Pharmacophores_- Thierry Langer
  10. Tutorial Pharmacophores – Thierry Langer
  11. QSAR_modelling – Mariia Matveieva
  12. Multiple-instance learning – Pavel Polishchuk
  13. De_novo_design – Pavel Polishchuk
  14. QSAR tutorial – Alina Kutlushina + Setup conda environment for SPCI and CREM + data logBB.sdf
  15. De novo CREM tutorial – Pavel Polishchuk + datafiles and notebooks
  16. Molecular Modelling intro – Karel Berka
  17. Molecular Docking intro – Karel Berka
  18. Is lipid membrane druggable? Insights from MD – Semen Yesylevskyy
  19. Moleculae Docking basic tutorial – Karel Berka
  20. Automatic local docking tutorial – setup and run – Pavel Polishchuk + docking tutorial data
  21. High throughput MD tutorial – Aleksandra Ivanova + command list
  22. Challenge – Pavel Polishchuk

Useful software links from IMTM – Pavel Polishchuk_group

Materials from previous workshops are available at
https://old.fch.upol.cz/en/research/conferences-workshops/5add/, or
https://old.fch.upol.cz/en/research/conferences-workshops/4add/, or
at our YouTube channel https://www.youtube.com/playlist?list=PLRGiGr8c-LlKaWGyMjEnnLV_iM9IvdxKU. 

Challenge

Try to solve our Ligand selection problem – will you be able to find the actives from the ligand pool or generate a new one?

Participation in the Challenge is an exam requirement for Advanced Rational Drug Design (KFC/ADD – 4 ECTS credits)

List of Registered Participants

Once you know that you cannot arrive, please tell us at karel.berka@upol.cz, so we can change you for online registration instead.

  1. Anita Ament – Palacky University Olomouc, CZ
  2. Jan Beránek – University of Chemistry and Technology, Prague, CZ
  3. Krishnendu Bera – Masaryk University Brno, CZ
  4. Indu Bhushan – Institute of Biophysics, Masaryk University, Brno, CZ
  5. Valerio Brando – Università degli studi di Napoli Federico II, IT
  6. Adam Bubík – Masaryk University Brno, CZ
  7. Lucia Iľkovičová – Masaryk University Brno, CZ
  8. Tomas Jelinek – Czech Technical University, Prague, CZ
  9. Jakub Juračka – Palacky University Olomouc, CZ
  10. Nina Kadášová – Palacky University Olomouc, CZ
  11. Leonid Kikot – Selvita S.A., PL
  12. Mikuláš Klenor – Institute of Organic Chemistry and Biochemistry, Prague, CAS, CZ
  13. Artem Kokorin – University of Luxembourg, LU
  14. David Kopečný – Palacky University Olomouc, CZ
  15. Katarzyna M. Krupka – University of Wroclaw, PL
  16. Natalia Kulik – Institute of Microbiology, Czech Academy of Sciences, Prague, CAS, CZ
  17. Laura Landolfi – Università degli studi di Napoli Federico II, IT
  18. Martin Lepšík – Institute of Organic Chemistry and Biochemistry, Prague, CAS, CZ
  19. Jan Macháň – Palacky University Olomouc, CZ
  20. Simona Martikánová – Palacky University Olomouc, CZ
  21. Dominik Martinát – Palacky University Olomouc, CZ
  22. Miriama Mateášová – Masaryk University Brno, CZ
  23. Guzel Minibaeva – Palacky University Olomouc, CZ
  24. Dominik Prager – Palacky University Olomouc, CZ
  25. Bensadok Raoula – University Of Science And Technology Houari Boumediene, DZ
  26. Hanna Severina – National University of Pharmacy, Kharkiv, UA
  27. Jan Stehlík – Palacky University Olomouc, CZ
  28. Katerina Storchmannova – Palacky University Olomouc, CZ
  29. Anna Špačková – Palacky University Olomouc, CZ
  30. Guglielmo Tedeschi – University of Chemistry and Technology, Prague, CZ
  31. Vojtěch Vařečka – Masaryk University Brno, CZ
  32. Náth Vozábal – Masaryk University Brno, CZ

Cost and Accommodation

There is no registration fee, also coffee breaks and partially workshop dinner is covered by our sponsors.

Accommodation is not provided by the organizers, but here are several places for consideration depending on your budget:

Accommodation and Dining Services of the Palacky University – https://skm.upol.cz/en/  – ~300-1000 CZK/night

Long Story Short Hostel – http://www.longstoryshort.cz/  – ~400-1000 CZK/night

Hotel Arigone – http://www.arigone.cz/en/ – ~2 300 CZK/night

and, of course, there is plenty of AirBnB places in “UNESCO jewel” city of Olomouc – https://www.airbnb.cz/s/Olomouc–%C4%8Cesk%C3%A1-republika 

If you have any questions, please send them to karel.berka@upol.cz 

Sponsors