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4th Hands-on Computational Enzyme Design Course

29 MAY – 1 JUNE, 2023

About the course

Do you need to engineer your protein of interest? Do you wish to employ user-friendly one-stop-shop software tools for the design of mutations and libraries, but do not want to spend time on tedious installations or use the Unix command-line? This interactive course will provide essential theory on different areas of enzyme engineering, and hands-on experience with several software tools suitable for mining new enzymes, engineering the activity, specificity, enantioselectivity, stability, and solubility of enzymes.

You will have the chance to learn from the developers or experienced users of those tools, and discuss the optimal ways to set-up calculations and adequately interpret the results. At the end of this 4-day course, you will be able to design different properties of proteins for your academic research or commercial applications on your own.

Software and databases coveredAlphaFillAlphaFoldCalFitter, Caver, CaverDockCaver Web, EnzymeMiner, ESMFold, FireProt, FireProtASR, FireProtDB, HotSpot WizardLoopGrafter, ProteinMPNN, Solubis, SoluProt and SoluProtMutDB. Our web-tools integrate multiple individual software, and altogether, you will get automated access to more than 50 computational methods and 15 databases.

Who should participate

The course is primarily meant for protein and metabolic engineers with no prior experience in computer modeling and bioinformatics. The experts willing to broaden their current computational protein design toolbox will also benefit from this course. Doctoral students, postdocs, and staff members from both academia and companies are welcome.

Previous editions

The 1st Hands-on Computational Enzyme Design Course was hosted in the classical in-person format and took place in Brno, Czech Republic, in 2020. We had more than 30 participants from 12 countries, about 70% from academia (ex.: Zurich University, KTH Royal Institute, Georgia Institute of Technology) and 30% from industry (ex.: Pfizer, Novartis Pharma, Johnson & Johnson).

The 2nd and 3rd Hands-on Computational Enzyme Design Course took place online in May 2021 and May 2022. In the last edition, we had more than 60 participants from 26 countries, also coming from academia (60%) and industry (40%), and we granted 3 need-based scholarships that covered the participation fees.

The participants learned the background theory of computational enzyme design, practiced the exercises provided and worked on their own problems of interest, always assisted by our team of experts. Knowledge and experience were exchanged in a friendly and interactive environment. The feedback was extremely positive in both on-site and online editions. Here is a selection of testimonies from the participants:

  • Excellent course set up! It helped me to understand more the bioinformatics tools and encouraged me to use them in the future. (Academia)
  • ‌This course gave a very interesting overview of the available methods (…) The organization was superb, the lecturers were extremely approachable and the information provided was very relevant. Would recommend it to everybody who is looking for an introduction to computational enzyme design. (Academia)
  • ‌‌The course is a very good introduction to computational enzyme engineering for non-bioinformaticians. The open discussions and useful computer exercises gave me a better understanding of the field (…) Besides the quality of the course contents, I have to say the social program and hospitality of the organizers were superb. I would definitely recommend it! (Academia)
  • Interesting tools, well-planned program, and nice people! I’d highly recommend participation in this course if you are looking to learn about the impressive range of online tools developed at the Loschmidt Laboratories. (Industry)
  • ‌Excellent organization and incredibly motivated tutors; great way to familiarize yourself with computational approaches for enzyme engineering. (Industry)
  • Overall I was highly impressed by the great organization of this course. Everything was prepared well in order to avoid technical issues successfully. I mostly appreciated that the tutorials were recorded and could be played and paused individually. There was always enough time to follow the tutorial and the discussion of open questions. (Industry)

This year we are hosting a hybrid format, which will bring the many advantages of the in-person course, such as improved interactivity, networking, and a vast social program, but keeping the online option for those who prefer to attend remotely.

Three pillars of the course


Theoretical lectures will cover the scientific background and state-of-the-art. The essence of each field required to understand the theory behind the studied tools will be presented.


„Learning by doing“ is the most efficient and enjoyable way to learn. The tool developers will guide you individually through the tutorials, interact, and discuss.


It is pleasant and useful to meet peers working on similar research topics from all over the world. Networking will take place at the opening and during the breaks.


Barbora Kozlíková
Biomolecular visualisations
David Bednář
Mining novel enzymes in databases
Faraneh Haddadi
Machine Learning for Protein Engineering
Jan Mičan
Protein-Protein Interface Design
Jan Velecký
Machine Learning for Protein Engineering
Jana Horáčková
Molecular Docking and Dynamics Simulations
Jiří Damborský
computational enzyme design
Joan Planas-Iglesias
sequence similarity search strategies
Miloš Musil
engineering of protein stability
Ondřej Vávra
Design enzyme tunnels and channels
Pavel Kohout
Machine Learning for Protein Engineering
Petr Kabourek
IT specialist
Petr Kouba
Machine Learning for Protein Engineering
Saltuk M. Eyrilmez
Structure-Based Virtual Screening
Sérgio Marques
Engineering catalytic activity
Stanislav Mazurenko
design by machine learning



The course will have the duration of 4 days (29 May – June 1, 2023), from 9 am to approximately 6:00 pm (Brno time, CET).

The program will be composed of a main scientific part, with theoretical lectures, hands-on sessions, and user-personalized cases. For the latter, the participants will apply the learned protocols to their own proteins of interest. It will also include time for discussions, networking and a vast social program, with coffee breaks, lunches, dinners, and a cultural tour.


Main topics that will be covered:

  • Mining and analysis of novel enzymes
  • Engineering protein stability and solubility
  • Engineering enzyme activity and specificity
  • Machine learning applied to protein engineering (NEW!)

The program also includes three “User cases” sessions, where the participants will practice the tools on their own systems of interest, always with our assistance.

Keynote lectureComputational enzyme design
TheoryMining and analysis of novel enzymes
        Hands-onIdentification of novel enzymes
        Hands-onHomology modelling and design of libraries
TheoryEngineering protein stability and solubility
        Hands-onDesign of stable proteins
        Hands-onAnalysis of soluble proteins
TheoryEngineering enzyme activity and specificity
        Hands-onModelling protein-ligand complexes
        Hands-onAnalysis of ligand pathways
        Hands-onRational loop grafting
        TheoryTunnel claculation with CAVER
TheoryMachine learning in biochemistry
        Hands-onML-based prediction of enzyme properties
        Hands-onStructure modelling with ML-based tools
SpecialEnantis: software and services


The participants will have many opportunities to expand their professional networks, socialize, and explore interesting cultural sites.

We include in the program a welcome reception, a gala dinner, as well as all lunches and coffee breaks. The cultural program includes a guided tour in the center of Brno and a visit to the Mendel Museum.


The 4th edition of the course will have the in-person format, taking place in Brno, Czech Republic, at the University Campus Bohunice (Masaryk University). This may be changed in case new severe restrictions will be enforced due to the COVID-19 pandemic.


This campus is known to be the largest project in the domain of university education in Central Europe. The campus hosts the Faculty of Science and Faculty of Medicine under a single roof. The course will be running in a modern computational laboratory with the necessary facilities.


The second-largest city in the Czech Republic. Fourteen universities and 90 000 students make it a pulsing “organism”. Brno is a city of rich culture, beautiful architecture, many coffee houses, restaurants, and green parks. It is the 6th most attractive city for students, according to the world-ranking. Brno was home to world-famous Gregor Mendel, the father of genetics.


The registrations are now open. Early-bird discounts apply.

The course has limited numbers of participants in-person and online. After your registration, your participation has to be confirmed. Do not miss your chance and register ASAP! To register click on the button below “I want to apply”.

The invoice will be issued based on the information provided during the registration.

Until 31 March, 2023
In-person1200 EUR2300 EUR
Online450 EUR860 EUR
Until 30 April, 2023
In-person1550 EUR3000 EUR
Online580 EUR1120 EUR

The in-person registration fees include:

  • Attendance to all scientific sessions
  • Course materials: slides of the theoretical lectures, step-by-step protocols, useful tips & tricks, relevant literature
  • Welcome reception and gala dinner
  • All lunches and coffee breaks
  • Guided city tour
  • Guided tour to Mendel Museum
  • Graduation certificate

Not included: accommodation, travel expenses.

The in-person format enables extended opportunities for scientific discussions and networking.

The online registration fees include:

  • Attendance to all scientific sessions
  • Course materials: slides of the theoretical lectures, step-by-step protocols, useful tips & tricks, relevant literature
  • Graduation certificate


We promote education above all. For this reason, we have scholarships available to i) students with fewer resources, and ii) scientists affected by armed conflicts, such as the one occurring in Ukraine. These scholarships will cover the registration fees for the online participation.

To apply, send to Šárka Nevolová (nevolova.sarka@gmail.com): 1) a motivation letter, and 2) your CV. In the motivation letter, you should describe why you are interested in this course and justify the need for the scholarship. To pre-reserve your seat, you have to register and add a note that you want to apply for the scholarship (use the button above).

The application deadline is 31 March 2023. The awardees will be announced by 15 April 2023.


In addition to the aforementioned scholarships, the COST Action COZYME CA21162, supported by COST (European Cooperation in Science and Technology), may also fund the participation of several trainees.


The participants should arrange for their own accommodation.

Single and double rooms are pre-booked in the HOTEL UNIVERSITY BRNO ***, which is located approximately 15 min trolley bus ride from the venue. The participants of the course have a secured room rate of €50/ night including breakfast. The rooms will be pre-booked till February 28th. Please mention the group code “Academy”.

We can recommend also OREA Hotel Voro Brno ***, which is located approximately at 25 min bus ride from the venue. The participants of the course have a secured room rate of €57/ night including breakfast. Fifteen single rooms will be pre-booked till May 4th. Use this link to book your accommodation and mention the code “COURSE2023”.

Further options are apartments located within the walking distance from the venue: In Apartments, Violet Apartment, Office Apartments, and Penzion Levandule

Contact us