SUMMER SCHOOL OF MOLECULAR DYNAMIC SIMULATIONS ANALYSIS WITH MOLECULAR PROBES – 22-25 VI 2020

ABOUT THE SCHOOL

Molecular dynamics simulations are widely used as a versatile research method. Many additional tools were developed to facilitate and extend analysis of MD simulations. AQUA-DUCT is one of the unique tools, that reverses the standard approach of describing the evolution of macromolecules’ dynamics. Instead of their atoms’ movement analysis, it enables an investigation from the perspective of “intramolecular voids”. To achieve this goal, AQUA-DUCT samples macromolecules’ dynamics employing molecular probes – small entities in simulations (most frequently water molecules, but it could be any solvent, co-solvent, ions, or other ligands). The small molecules are used as specific chemical probes. The mixed “ligands-tracking” and “local-distribution” approaches implemented in AQUA-DUCT allow discrimination between functionally relevant compartments, and provide direct access to information about the active site, potential hot-spots, functional residues (gates, anchoring residues, filters, etc.), the network of internal transportation pathways, and functional voids and cavities. Besides that, it can facilitate the drug design process.

The school will provide an opportunity to learn basic and advanced analysis performed with AQUA-DUCT (hands-on), and additionally to perform preliminary analysis or set properly the system on their own interests. Participation is free of charge.

Requirements

At least basic knowledge of Linux system and PyMol
Knowledge of classical molecular dynamics simulations (any software)

Literature

AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective. Magdziarz T., Mitusińska K., Bzówka M., Raczyńska A., Stańczak A., Banas M., Bagrowska W., Góra A., Bioinformatics 2019, 1–3.  OPEN ACCESS
AQUA-DUCT a ligands tracking tool. Magdziarz T., Mitusińska K., Gołdowska S., Płuciennik A., Stolarczyk M., Ługowska M., Góra A., Bioinformatics 2017, 33 (13): 2045-2046.  OPEN ACCESS

Examples of AQUA-DUCT application

Subramanian K., et al., Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase. Biomolecules (2019) 9(6), 212. OPEN ACCESS
Subramanian K., et al., Modulating D-aminoacid oxidase (DAAO) substrate specificity through facilitated solvent access. PLoS ONE (2018) 13(6):e0198990. OPEN ACCESS
Mitusińska K., et al., Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking. Biomolecules (2018) 8(4), 143. OPEN ACCESS

PRELIMINARY PROGRAMME

Day One – Monday 22 June 2020 – Introduction to AQUA-DUCT

09:00 – 10:00 Registration & Welcome address
10:00 – 10:45 Lecture 1: AQUA-DUCT – general information, functionality, workflow vol.1
10:45 – 11:00 Refreshment Break
11:15 – 12:00 Lecture 2: AQUA-DUCT – general information, functionality, workflow vol.2
12:00 – 13:00 Lunch
13:00 – 14:30 Hands-on 1: Introduction to AQUA-DUCT calculations
14:30 – 14:45 Refreshment Break
14:45 – 16:15 Hands-on 2: Introduction to AQUA-DUCT calculations
Free Time – Networking

 Day Two – Tuesday 23 June 2020 – Molecular probes applicability in protein engineering

08:45 – 09:00 Day briefing
09:00 – 09:45 Lecture 3: Molecular probes applicability in protein engineering
09:45 – 10:00 Refreshment Break
10:00 – 12:00 Hands-on 3
12:00 – 13:30 Lunch
13:30 – 15:30 Hands-on 4
Free Time – Optional excursion

 Day Three – Wednesday 24 June 2020 – Molecular probes applicability in drug design

08:45 – 09:00 Day briefing
09:00 – 09:45 Lecture 4: Molecular probes applicability in drug design
09:45 – 10:00 Refreshment Break
10:00 – 12:00 Hands-on 5
12:00 – 13:30 Lunch
13:30 – 15:30 Hands-on 6
Free Time – Networking

Day Four – Thursday 25 June 2020 – Bring your own data + Q&A/Round Table

08:45 – 09:00 Day briefing
09:00 – 10:00 Participants flash presentations (5 min each participant)
10:00 – 10:30 Refreshment Break
10:00 – 12:00 Hands-on 7 Working on your own data
12:00 – 13:30 Lunch
14:00 – 16:30 Hands-on 8 Working on your own data + Q&A
Free Time – Networking

REGISTRATION

REGISTRATION DEADLINE
15 March 2020

CHOSEN PARTICIPANTS WILL BE NOTIFIED BY
1 April 2020

Submission deadline for data samples for the hands-on sessions
15 April 2020

Registration includes:
Access to IT infrastructure (no need to bring own computers)
Course materials
Coffee breaks
Lunches

Not included:
Accommodation
Travel to and from the venue
Dinners outside the organized events

PLEASE REGISTER HERE 

SELECTION CRITERIA

All applicants should upload a motivation letter containing a short description of their current research and a CV with a list of publications (if available).
Short information about the system of interest
Master students should, in addition, provide a recommendation letter from their tutor.
Incomplete applications will not be considered for the selection process.
We will maintain a balance between genders and between countries in Europe. Please note, that the number of participants is strongly limited (12).

 

ORGANIZERS

 

 

The Tunneling Group was established in June 2014 at The Biotechnology Centre as an independent research group.

The main activity of the group borders the fields of molecular biology and computational chemistry. We are using an advanced theoretical approach to investigate the properties of various enzymes, to design biologically active compounds, and to help experimentalists interpret their results. We are also developers of the scientific software, AQUA-DUCT and BALCONY. More about group activity on the official site.

Contact

Artur Góra
Email: a.gora@tunnelinggroup.pl
Phone: (+48) 32 237 16 59

or AQUA-DUCT team

Email: info@aquaduct.pl

VENUE

THE BIOTECHNOLOGY CENTRE

The Biotechnology Centre was established at the Silesian University of Technology (SUT) in 2006. It was created as an interdisciplinary platform to engage researchers from all departments of the SUT working in the fields of biotechnology and molecular biology. The Biotechnology Centre is also a partner of the BIO-FARMA consortium formed in April 2007 by the SUT, the Centre of Oncology, the Silesian Medical University, and the University of Silesia, thereby providing easy access to various collaborations and interdisciplinary projects.
The existing infrastructure of the Biotechnology Centre ensures general availability of state-of-the-art scientific equipment including a supercomputing centre; RT-PCR; UHPLC; UV-VIS, FT-IR, FT Raman, MS, and NMR spectrophotometers; light, fluorescent, and confocal microscopes; atomic force microscopy (AFM); nucleic acids and protein structure/function analysis equipment.

THE SILESIAN UNIVERSITY OF TECHNOLOGY

The Silesian University of Technology (SUT), is the oldest technical university in the region and one of the most prestigious in Poland.
It has received the prestigious Research University status this year. It was established in 1945 as a scientific and educational facility for Upper Silesia, the most industrialized area in Poland, and one of the most industrialized in Europe.
For 75 years of its history, it has always been a public institution, playing a cultural and opinion-forming role in the region.
In 2019, the University obtained the status of a Research University as one of 10 universities in Poland.

 

 

ACCOMMODATION
The hotels in walking distance from Biotechnology Centre are:
Hotel Diament Economy Gliwice
Hotel Diament Plaza Gliwice
Hotel Royal
Qubus Hotel Gliwice
Gold Hotel Silvia

TRANSPORT

The Silesian University of Technology is located near the centre of Gliwice, approximately 1.5 km from the Central Railway Station (15 min. walk, 7 min. by car), a taxi stop and Bus Station. Gliwice has an efficient communication system, which provides convenient local and international connections.
Gliwice has direct access to 2 major Polish motorways:
● A1 – north-south
● A4 – east-west

The nearest airports to Gliwice are: in Katowice (40km), Kraków (100km), Wrocław (170km) and Ostrava (Czech Republic, 95 km).

• Katowice-Pyrzowice Airport (highly recommended)
The nearest airport located within 30 minutes by car to Gliwice.
http://www.katowice-airport.com/

You can travel from the airport to Gliwice by direct bus – AP1 line  https://rj.metropoliaztm.pl/rozklady/1-ap1/?lang=en

• Kraków-Balice Airport
An airport located further – 3,5 hours by train or 1,5 hours by car to Gliwice.
http://www.krakowairport.pl/pl/

• Wrocław Airport
An airport located in the neighbouring region, within ~2 hours by car, 2,5 hours by train to Gliwice.
http://airport.wroclaw.pl/

• Ostrava Airport
An airport located in the Czech Republic, within 1 hour by car to Gliwice.
http://www.airport-ostrava.cz/en/

• Warszawa Airport (Fryderyk Chopin Airport)
An airport located in our capital, about 323 km from Gliwice:
https://www.lotnisko-chopina.pl/en/index.html

ABOUT THE AREA

Gliwice is a medium-sized city of nearly 200 thousand inhabitants. The city is an important scientific, research and design centre in Poland. Thanks to the Silesian University of Technology, it is the second largest (after Warsaw) agglomeration of technical intelligence in Poland. During the last 20 years, Gliwice has transformed from a city based on heavy industry into a leader in new technologies.
Apart from that, Gliwice is also well known for its cultural life. A lot of festivals, concerts, exhibitions and other art activities take place in the town. Numerous famous Polish artists and other interesting people (e. g. Nivea cream inventor) originally came from Gliwice. Results of many surveys show that it is one of the most attractive cities in Poland.
The city has a rich history of nearly 800 years. Throughout that time it has undergone several historical transformations. It was ruled by the Silesian Piast Monarchy, the Kings of Bohemia, the Austro–Hungarian Empire, Prussia and Germany, until the city has again become a part of Poland in 1945.
Gliwice is a unique place, where tradition, multicultural heritage, science and modernity intermingle, creating its one-of-a-kind atmosphere of an attractive place to study and live.

Useful links:
 https://gliwice.eu/en