TRAINING SCHOOL for Young Researchers & Innovators

Training school on “Computer-aided tools in the study and therapy of bacterial drug resistance” is organized in Lisbon within the framework of the COST Action, in connection with the first EURESTOP meeting. The training school is ideally suited for YR&Is (i.e., under the age of 40) but it is open to all EURESTOP members.

1st Training School
Lisbon, 23-25 January 2023

CA21145 Training school in Bioinformatics and Computational tools in antibacterial research

Universidade Lusófona de Humanidades e Tecnologias Lisbon, Portugal

Welcome to Lisbon

On behalf of the Organizing Committee, we would like to thank you for attending the Training School of COST Action CA21145.

The aim of the Training School is to pass on to the young researchers the expertise and knowledge of the working groups activity carried out within the Action.

At the same time, the Training School is an opportunity to update on th state of the art as well as to highlight the importance of an interdisciplinary approach.

We sincerely hope that you will enjoy the Training School, exchange new ideas and promote future collaborations.

We look forward to welcoming you at the 1st Training School!


Location: Lisbon, Portugal 23-25 January 2023
Venue: CBIOS, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa


Scientific Committee:

Mattia Mori (Italy) – Action Chair
Patricia Rijo (Portugal) – Vice Chair
Cristina Nativi (Italy) – Science Communication coordinator
Priyanka Sahariah (Iceland) – Grant Awarding coordinator
Dana Reichmann (Israel) – WG1 Leader
Younes Smani (Spain) – WG2 Leader
Carole Devaux (Luxembourg) – WG3 Leader

Local Organizing Committee:

Patrícia Rijo (Local Organizer)
Vera Isca (Portugal)
Márcia Filipe (Portugal)
Gabrielle Bangay (Portugal)
Daniel Santos
Ana Mourato
Andreia Rosatella

Management: Carolina Altilia – COST Action CA21145 –

Practical Information 1st Training School of COST Action CA21145 (Lisbon, 2023)


The Training School will be held at:
CBIOS – Universidade Lusófona de Humanidades e Tecnologias Campo Grande, 376
1749-024 Lisboa

Telephone: (+351) 217 515 500

The best way to get there is either by bus, metro or taxi. All means of transportation are available at the airport.

BusIf you decide to go on a bus, you need to catch 783 AMOREIRAS at the airport, and then catch another bus 717 or 767 at “Júlio de Matos”. Get off after 2 stops: both 717 and 767 stop in front of the University. You can buy your ticket inside the bus. Each ticket is 1.85 € for one journey. If you decide to return by bus, you will have to buy two tickets.

Metro/subwayIf you decide to catch the metro at the airport, you must go to Alameda (Red Line) and change to the Green Line, heading to Telheiras. You must get off the metro at Campo Grande, and then walk to the University Lusófona.

The ticket price is 2.5 EUR. Daily tickets for all transportations (bus and metro) are available at the price of 2 EUR found inside the metro.

TaxiDepending on traffic, the journey to the city center is quick, costing around 20 EUR, including luggage fees. If you choose this mean of transportation, make sure the meter is turned on at the beginning of the journey and always ask for a receipt/invoice.

CA21145 Action Summary

The emergence and spread of drug-resistant bacteria is an important health and socioeconomic threat with global dimensions, which is developing towards an emergency/pandemic crisis. No drugs are available to address the disease, and diagnostic tools are poorly effective. This negatively impacts the treatment and survival of critically ill patients. As such, drug-resistant bacteria may spread outside hospital settings, representing a critical risk for the global population.

Current research in this field is highly fragmented and mostly monodisciplinary, thus limiting the development of innovative diagnostic and therapeutic solutions. This COST Action will bring together industrial and academic European scientists with different skills and expertise in a multidisciplinary and concerted initiative. The Action will combine disciplines such as chemistry, physics, bioinformatics, genetics, biology, immunology, and medicine in understanding the genetic and molecular bases of bacterial drug resistance, developing innovative diagnostic tools, and delivering lead/pre-clinical candidates, antibody-based therapies, and clinical-ready repurposed drugs towards the personalized treatment of drug-resistant bacterial infections. The further challenge of the Action is to enhance networking among European scientists and to increase the competitiveness of European research by promoting the exploitation of translational research outcomes, e.g., by the creation of novel SMEs.

Finally, by knowledge creation and sharing, the Action will train a new generation of young scientists skilled in the multiple aspects related to bacterial drug resistance. Career development of Young Researchers and Innovators and research impulses in Inclusiveness Target Countries (ITC) will be considered as a priority in the Action.


COST is a unique means for European researchers, engineers and scholars to jointly develop their own ideas and new initiatives across all fields of science and technology through trans-Europe networking of nationally funded research activities.


The first Training School of the Action will be an important moment for the formation of the Young Researchers & Innovators as well as to start building a team of YR&Is that will interact closely within the framework of the CA21145 Action.

The program will focus on the broad use of computers in current research in the field of bacterial drug resistance, including molecular simulations (either ligand- and structure-based) and genomics/proteomics analyses.

The training school will combine oral lectures by experts in the field with practical application of bioinformatics and computational tools. The daily program will combine oral lectures by experts in the field with practical applications on topics and tools described and discussed in the oral lectures.

The main aim of the training school is to provide YR&Is with a general background on computational and bioinformatics tools, which might be relevant at the beginning of a research project. Trainees can also share their current research problems with the trainers and the audience of the training school to discuss on possible solutions.


23 January, 2023:

Ligand- and Structure-based approaches in drug design

Trainers: Daniel Santos (Portugal) and Petko Alov (Bulgaria)

08:30 09:00   Registration of participants

09:00 09:15   Opening:

L. Monteiro Rodrigues (CBIOS Director),
Patrícia Rijo
Local organizer
Mattia Mori (Action Chair)

09:15 – 13:00  Session #1 Daniel Santos and Petko Alov
13:00 – 14:00  Lunch break
14:00 – 17:30  Session #2 Daniel Santos and Petko Alov

Daniel Santos: Hands-on approach for discovering efflux modulators using a structure- based approach
Petko Alov: Ligand-based in silico approaches for evaluation of ADME/Tox properties of biologically active compounds

24 January, 2023:

Molecular dynamics and metadynamics simulations

Trainers: Alejandro Seco (Spain) and Daniel Conde Torres (Spain)

09:00 13:00  Session #1 Alejandro Seco and Daniel Conde Torres

13:00 – 14:00  Lunch break
14:00 – 17:30  Session #2 Alejandro Seco and Daniel Conde Torres

Alejandro Seco: Molecular Dynamics simulations to explore innate immune systems peptides and their cell membrane interactions: SuPepMem database
Daniel Conde Torres: Insights into the mechanisms of antimicrobial peptide action through metadynamics simulations

  • Introduction to the use of molecular dynamics simulations in the study of antibiotic- resistant bacterial infections

  • Hands-on case study: Coarse-grained MD simulation of an antimicrobial peptide interacting with a bacteria model membrane. Setting up the simulations and utilizing supercomputer resources.
  • Analysis and interpretation of the results from MD simulations
  • Utilizing augmented and virtual reality visualization tools for enhanced analysis and understanding of the simulation results

25 January, 2023
Proteomics data analysis in microbiology

Trainer: Dana Reichmann (Israel)

09:00 13:00  Session #1 Dana Reichmann
13:00 – 14:00  Lunch break
14:00 – 17:30  Session #2 Dana Reichmann

Dana Reichmann: Applications of quantitative and structural proteomics in microbiology
Dana Reichmann:
Introduction into proteomics data analysis

Meals Information

The local organizing committee has agreed on meals for lunches and the social dinner. Please let us know if you want to adhere to this initiative with a fixed (and good) price through the online form. Please fill in the form no later than Thursday 19 January 2023, 02:00 pm CET time. After this deadline, we won’t be able to guarantee access to meals at the agreed conditions. Lunches will be served in the local canteen at Lusofona University, while the social dinner will be organized in a restaurant in the nearby the Meeting location (information in the form).


  • If you agree to participate in organized lunches and the social dinner, you are kindly requested to pay for the respective fee at the registration desk by cash (no credit card) during your registration at the event.
  • Participants attending also the subsequent meeting will receive an additional form for meals options during the meeting. They are kindly requested to fill in both forms with their preferences.

MEALS during the Training School_form

MEALS during the Meeting_form