4th Advanced in silico Drug Design workshop/hackathon 2019
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)
Lecturers
doc.
Karel Berka, dr.
Pavel Polishchuk,
Mariia Matveieva, dr.
Václav Bazgier (UPOL)
Registration
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.
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
| 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
- Pavel Banáš, Palacky University Olomouc, CZ
- Hadley Clayton, University of South Africa, ZA
- Martin Drastík, Charles University, CZ
- Sergei Evteev, Lomonosov Moscow State University, RU
- Adrià Gil-Mestres, CIC-nanoGUNE, ES
- Pavlo Hrab, Ivan Franko National University of Lviv, UA
- Ondřej Hrabina, Palacky University Olomouc, Institute of Biophysics of CAS, CZ
- Artem Kokorin, Kazan Federal University, RU
- Viktoria Koshcheenko, Taras Shevchenko National University of Kyiv, UA
- Miroslav Kvasnica, Palacky University Olomouc, CZ
- Alina Lavrova, Shemyakin-Ovchinnikov Institute of bioorganic chemistry, Russian Academy of Sciences, RU
- Nadiia Lekhniuk, Ivan Franko National University of Lviv, UA
- Radek Majdloch, IOCB Prague/Palacky University Olomouc, CZ
- Aleksandr Malyshev, Lomonosov Moscow State University, School of Medicine, Pharmacy Department, RU
- Michaela Melikova, Palacky University Olomouc, CZ
- Vijay Miriyala, IOCB Prague, CZ
- Olena Mokshyna, Palacky University Olomouc, CZ
- Jahn Nitschke, Universität Konstanz, DE
- Alexey Noev, MIREA-Russian Technological University, RU
- Jozef Pecha, Palacky University Olomouc, CZ
- Ekaterina Shevchenko, Sechenov University, RU
- Martin Šrejber, Palacky University Olomouc, CZ
- 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
