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5th Hands-on Computational Enzyme Design Course

12 - 14 FEBRUARY, 2024

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 3-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 covered: Aggreprot, AlphaFillAlphaFold, Caver, CaverDockCaver Web, ChannelsDB, EnzymeMiner, ESMFold, FireProt, FireProtASR, FireProtDB, HotSpot WizardLoopGrafter, ProteinMPNN, RF Diffusion, 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 following editions of the Hands-on Computational Enzyme Design Course took place online in May 2021 and May 2022, and the 4th edition was held in hybrid mode in May 2023. Here we had nearly 60 participants from 19 countries, also coming from academia (80%) and industry (20%), and we granted 2 scholarships.

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, online)
  • ‌‌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, in-person)
  • ‌Excellent organization and incredibly motivated tutors; great way to familiarize yourself with computational approaches for enzyme engineering. (Industry, in-person)
  • 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, online)
  • This course was extremely well organized, and covered the basics and more advanced bioinformatics tools. I can now more confidently use these tools and apply them to my own enzymes! (Academia, online)
  • This is one of the best courses that I have taken in my long scientific career. All instructors are highly qualified and not only experts in their respective areas, but also have insights and can address any challenge in different research areas. All scientists and instructors are very friendly yet very diverse, which enriches the cultural diversity (…). This is a highly recommended course designed and developed by one of the leading groups in Protein Engineering in Europe and Worldwide. (Academia, in-person)
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 3 days (12 – 14 February, 2024), approximately from 9 am to 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.


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

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


The 5th edition of the course will take place online.


The registrations will be open between 15 October and 15 December 2023. Early-bird discounts apply.

The course has limited numbers of participants. 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 30 November, 2023
400 EUR700 EUR
Until 15 December, 2023
550 EUR850 EUR

The 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.

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 first and add a note that you want to apply for the scholarship (use the button above).

The scholarship awardees in 2024 are:

  • Marija Stefanović (University of Belgrade)
  • Raja Singh Rawal (CSIR-Indian Institute of Petroleum)
  • Visnja Kosic (University of Belgrade)
  • Zara Bukhari (University of the Pacific)

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