5th Advanced in silico Drug Design workshop/challenge 2020


5ADD workshop/challenge (3.2.-7.2.2020) is focused on the use of in silico drug design tools and approaches in the drug design. We will 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-hands tutorials. Last day you can try your skills on ligand selection challenge.

Invited lecturers

prof. Thierry Langer (UniVie), dr. Lukáš Pravda (EMBL-EBI), dr. Timur Madzhidov (Kazan Federal U), Ivo Kabelka (CEITEC)

Lecturers and Organizers

doc. Karel Berka, dr. Pavel Polishchuk, dr. Olena Mokshyna, Mariia Matveieva, dr. Václav Bazgier, Martin Šrejber, Michaela Melíková (UPOL)

Registration

Register at https://forms.gle/UrXkU4wy3uvm1e2w5

Registration is open till 31st December 2019 or till the filling up of space

Attendance of the event is free of charge. Lecture room holds up to 36 seats. Registrations with poster presentations will be prioritized.

Venue

Palacky University Olomouc (UPOL)

Faculty of Science

tř. 17. listopadu 12

rooms 3.002 (tutorials/challenge), 3.003 (lectures)

Olomouc 77900

Czech Republic

Program

Monday3.2.2020 Basics
12:0012:30Registration and Wellcome
12:3013:30 Drug design intro (Berka)
13:3014:30Structural bioinformatics services at PDBe for drug design (Pravda) + PDBe-KB introduction (Pravda)
14:3015:00caffeine
15:0017:00Tutorial on the usage of PDBe services (Pravda)
17:0019:30Poster session
Tuesday4.2.2020 Ligand-based methods
9:009:45Chemical library design (Polishchuk)
10:0011:30Virtual screening (Polishchuk)
11:3011:40coffein
11:4012:30QSAR modelling (Mokshyna)
12:0013:00lunch break
13:0014:00Similarity search and QSAR tutorial (Polishchuk, Matveieva) 
14:0014:30kafe
14:3016:30Similarity search and QSAR tutorial - cont. (Polishchuk, Matveieva)
Wednesday5.2.2020 Towards the usage
9:0010:30 Deep Learning (Madzhidov)
10:30 11:00 fika
11:0012:00 Peptide design (Kabelka)
12:0013:00  lunch break
13:0014:00 Pharmacophore modelling (Langer) 
14:0014:30 7-methyltheophylline + photo
14:3017:00Pharmacophore - tutorial (Langer) - installation instructions
18:00 -- workshop dinner
Thursday6.2.2020Structure-based methods
9:0010:00Reaction modelling (Madzhidov)
10:0010:30 1,3,7-trimethylxanthine
10:3011:30 Molecular modelling intro (Berka) 
11:3012:30Molecular docking intro (Berka)
12:3013:30lunch break
13:3015:30Molecular docking tutorial  (Berka, Bazgier) 
15:0016:00CAS 58-08-2
16:0017:00Molecular docking into the structural ensemble (Berka)
18:00 19:00 Excursion to IMTM (Polishchuk)
Friday7.2.2020Challenge day
9:0015:00Challenge (Polishchuk)
15:0015:10Final word (Berka)

Challenge:

Try to solve our Ligand selection problem - will you be able to find the actives from the ligand pool? Participation in the Challenge is an 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 are available here.

Links to programs:

Posters

As a novelty this year, we will allow participants to present their own research through a poster session. Send abstracts of posters in 1-page format (template here) to email address: karel.berka@upol.cz with "5ADD poster" in the subject line.

Poster abstracts are linked below

List of Registered Participants

We have filled the limit of participants and we have now a waiting list, so if you are in the list and you cannot come, tell us immediately, so we can offer the spot further by line.

  1. Martin Balouch, UCT Prague, CZ - Liposomes: a prediction model for API/lipid behaviour
  2. Gizem Nur Duran, Marmara U, TR - Computational Construction of Neisseria Meningiditis
  3. Sergei Evteev, Insilico Medicine, RU
  4. Anastasia Fomina, Lomonosov MSU, RU - Search for small molecule binding sites in Flavivirus NS1 protein
  5. Enrico Gandini, U Milano, IT - Computational Studies of Antifreeze Peptides
  6. Mateusz JędrzejewskiWroclaw U Science and Technology, PL
  7. Lukáš Jeremias, Mendel U Brno, CZ
  8. Bola Khalil, U Vienna, AT
  9. Mateusz Jędrzejewski, Wroclaw U Science and Technology, PL
  10. Eva Karasková, Palacky U Olomouc, CZ
  11. Kristina Lantseva, Saint Petersburg State U, RU
  12. Nadiia Lekhniuk, Ivan Franko National U Lviv, UA
  13. Alexey Lisov, Moscow State U, RU
  14. Dominik Martinát, Palacky U Olomouc, CZ
  15. Michaela Melíková, Palacký U, CZ - In Silico Models of MRP Transporters
  16. Oleksandr Oksiuta, Inst Org Chem NAS Kiev, UA
  17. Valeriia Rezapova, ITMO U, RU
  18. Polina Rusina, Moscow State U, RU - STOP DOUBLE AGENT: prediction of novel CDK7 inhibitor activity by MD simulation
  19. Ankush Singhal, Max Planck Institute for Colloids and Interface, GE
  20. Iris Sokka, U Helsinki, FI - Improving the Potency of Auristatin Cancer Drugs by Virtual Structure Modifications
  21. Elina Smolkina, Moscow State U, RU - Computer-aided screening for LDH inhibitors with the use of structural filtration
  22. Ivanna Subtelna, Danylo Halytsky Lviv Med U, UA - Molecular docking, QSAR and compare analysis for derivatives of 2-arylamino-2-thiazoline-4-ones and 4-arylamino-5H-thiazol-2-ones.
  23. Anastasia Tikhonova, ITMO U, RU
  24. Marija Todorovska, U Ss Cyril Methodius, MK - In Vitro Antidiabetic Activity and In Silico Approach on Hypericum perforatum L. Hairy Root Cultures
  25. İlknur Yıldız, Marmara U, TR - Investigation on anti-Inflammatory Effects of Hypericum Perforatum L. Flavonoids with Molecular Docking to COXs and LOXs
  26. Artsemi Yushkevich, Belarusian State U, BL

Once you will know that you cannot arrive, please tell us, so we can accept those on the reserve list. 

Cost and Accommodation

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

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