4th Advanced in silico Drug Design workshop/hackathon 2019

4ADD 4ADD workshop/hackathon (21.1.-25.1.2019) is focused on the use of in silico drug design tools and approaches in the drug design and optimimization. We will cover both structure-based drug design (molecular docking, molecular dynamics, structural bioinformatics tools) and ligand-based drug design (QSAR, pharmacophores, deep learning). Hackathon on the last day is the best opportunity to try your skills on our ligand selection challenge.

Invited lecturers

prof. Thierry Langer (UniVie), dr. Per Larsson (UppsalaUni), dr. Thomas Evangelidis (IOCB&CEITEC)


doc. Karel Berka, dr. Pavel Polishchuk, Mariia Matveieva, dr. Václav Bazgier (UPOL)


Register at https://goo.gl/forms/OxbEE2pYSGF6ens93  Registration is closed Attendance of the event is free of charge. Lecture room holds up to 36 seats.


Palacky University Olomouc (UPOL) Faculty of Science tř. 17. listopadu 12 rooms 3.002 (tutorials/challenge), 3.003 (lectures) Olomouc 77900 Czech Republic


Monday 21.1. Basics
12:30 13:30 Drug design intro (Berka) - video
13:30 14:30 Virtual screening (Polishchuk) - video
14:30 15:00 caffeine
15:00 16:00 Chemical library design (Polishchuk) - video
16:00 17:00 Structure bioinformatics tools for drug design (Berka) - video 
Tuesday 22.1. Ligand-based methods
9:30 10:30 QSAR modeling (Polishchuk) - video
10:30 11:00 coffein
11:00 12:00 Deep learning (Evangelidis) - video
12:00 13:00 lunch break
13:00 15:00 Python basics, similarity search and QSAR tutorial (Polishchuk, Matveieva) - installation instructions
15:00 15:30 kafe
15:30 17:00 Deep learning tutorial (Evangelidis)
17:30 19:00 Excursion to IMTM (Polishchuk)
Wednesday 23.1. Towards the usage
9:30 10:30 De novo design (Polishchuk) - video
10:30 11:00 fika
11:00 12:00 in silico drug delivery optimization (Larsson) - video
12:00 13:00  lunch break
13:00 14:00 Pharmacophore modelling (Langer) - video 
14:00 14:30 7-methyltheophylline
14:30 17:00 Pharmacophore - tutorial (Langer), LigandScout capabilities, downloads: Linux, Windows, Mac, license 
18:00   workshop dinner - Restaurant Moritz 
Thursday 24.1. Structure-based methods
9:30 10:30 Molecular modelling (Berka) - video
10:30 11:00 1,3,7-trimethylxanthine
11:00 12:00 Molecular docking intro (Berka) - video
12:00 13:00 lunch break
13:00 13:50 Molecular docking tutorial  (Berka, Bazgier) 
14:00 14:30 CAS 58-08-2
14:30 17:00 Molecular docking with molecular dynamics tutorial (Berka, Bazgier)
Friday 25.1. Challenge/Hackathon day
9:30 15:00 Challenge (Polishchuk)
15:00 15:10 Final word (Berka)
Hackathon Challenge: Try to solve our Ligand selection problem - will you be able to find the actives from the ligand pool? Participation to hackathon is exam requirement for Advanced Rational Drug Design (4 ECTS credits)

Course Materials

Language of the event is English. All course material will be available at this webpage. Materials from previous workshops is available here.

List of Participants

  1. Pavel Banáš, Palacky University Olomouc, CZ
  2. Hadley Clayton, University of South Africa, ZA
  3. Martin Drastík, Charles University, CZ
  4. Sergei Evteev, Lomonosov Moscow State University, RU
  5. Adrià Gil-Mestres, CIC-nanoGUNE, ES
  6. Pavlo Hrab, Ivan Franko National University of Lviv, UA
  7. Ondřej Hrabina, Palacky University Olomouc, Institute of Biophysics of CAS, CZ
  8. Artem Kokorin, Kazan Federal University, RU
  9. Viktoria Koshcheenko, Taras Shevchenko National University of Kyiv, UA
  10. Miroslav Kvasnica, Palacky University Olomouc, CZ
  11. Alina Lavrova, Shemyakin-Ovchinnikov Institute of bioorganic chemistry, Russian Academy of Sciences, RU
  12. Nadiia Lekhniuk, Ivan Franko National University of Lviv, UA
  13. Radek Majdloch, IOCB Prague/Palacky University Olomouc, CZ
  14. Aleksandr Malyshev, Lomonosov Moscow State University, School of Medicine, Pharmacy Department, RU
  15. Michaela Melikova, Palacky University Olomouc, CZ
  16. Vijay Miriyala, IOCB Prague, CZ
  17. Olena Mokshyna, Palacky University Olomouc, CZ
  18. Jahn Nitschke, Universität Konstanz, DE
  19. Alexey Noev, MIREA-Russian Technological University, RU
  20. Jozef Pecha, Palacky University Olomouc, CZ
  21. Ekaterina Shevchenko, Sechenov University, RU
  22. Martin Šrejber, Palacky University Olomouc, CZ
  23. Vaishali Uniyal, Palacky University Olomouc, CZ
Once you will know that you cannot arrive, please tell us, so we can accept those on reserve list. 

Cost and Accommodation

There is no registration fee, also coffee breaks and partially workshop dinner are covered by ELIXIR CZ. Hackathon has been supported by BioSolveIT. Accommodation is not provided by the organizers, but here are several places for consideration depending on your budget: If you have any questions, please send them to karel.berka@upol.cz