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3rd Hands-on Computational Enzyme Design Course

30 MAY - 1 JUNE, 2022
Online edition

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 with the Unix command-line? This interactive course will provide the essential theory and hands-on experience on a number of web-based tools suitable for mining new enzymes, engineering the activity, specificity, enantioselectivity, stability, and solubility of enzymes.

You will have the chance to learn and discuss with the developers of these tools 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.

Web-tools covered: EnzymeMiner, HotSpot Wizard, FireProt, FireProtASR, FireProtDB, CalFitter, Caver Web, CaverDock, LoopGrafter, Solubis and SoluProt. Our web tools integrate 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 on-site format, and it took place in Brno, Czech Republic, in February 2020. We had more than 30 participants from 12 countries and 3 continents, about 2/3 from academia (ex.: Zurich University, KTH Royal Institute, Georgia Institute of Technology) and 1/3 from industry (ex.: DTU Biosustain, Pfizer, Novartis Pharma).

The 2nd Hands-on Computational Enzyme Design Course was held online in May 2021. We had more than 40 participants from 16 countries, also coming from both academia and industry.

The participants learned the background theory of computational enzyme design, practiced the exercises that we prepared and worked on their own problems of interest, always assisted by our team of experts. Knowledge and experience was 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)

The on-site edition included a wider range of tools, web-based and stand-alone, some of which cannot be covered on an online version (ex.: Blast, Swiss-Model, PyMOL, AutoDock Vina, FuncLib, AffiLib, Yasara, Caver, Caver Analyst). It also comprised an extensive social program that was more difficult to implement in the online version. This format of the course will be repeated in the future. If you are interested, subscribe to our newsletters and stay tuned.

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
Jan Štourač
Design of mutations and smart libraries
Jiří Damborský
computational enzyme design
Jiří Filipovič
High-performance computing
Jiří Hon
engineering protein solubility
Joan Planas-Iglesias
sequence similarity search strategies
Miloš Musil
engineering of protein stability
Ondřej Vávra
Design enzyme tunnels and channels
Rayyan Khan
Protein evolution and design
Sérgio Marques
Engineering catalytic activity
Stanislav Mazurenko
design by machine learning



The online workshop with be run live during 3 days (May 30–June 1, 2022), from 9 am to 6:00 pm (CET). The program will be composed of a main scientific part, with theoretical lectures and hands-on sessions. However, it will also include discussion rooms reserved for networking, exchange of experiences, contacts and cultural backgrounds. The latter will be promoted by a devoted platform.

Scientific program

Keynote lectureComputational enzyme design
TheoryMining and analysis of novel enzymes
        Hands-onIdentification of novel enzymes
        Hands-onHomology modelling and design of libraries
TheoryEngineering enzyme activity and specificity
        Hands-onModelling protein-ligand complexes
        Hands-onIdentification of enzyme tunnels
        Hands-onAnalysis of ligand pathways
        Hands-onRational loop grafting
TheoryEngineering protein stability
        Hands-onDesign of stable proteins
        Hands-onAnalysis of stability data
TheoryEngineering protein solubility
        Hands-onDesign of soluble proteins


The 3rd edition of this course is taking place online for safety reasons.


The registrations will be open between 15 March and 30 April, 2022. Early-bird discounts apply. The invoice will be issued based on the information provided during the registration. The course is limited to 50 participants, prioritized based on their registration order. Do not miss your chance and register now! Click on the “I want to apply” button below to register.

Till April 15th, 2022350 EUR650 EUR
Till April 30th, 2022450 EUR850 EUR

The registration fee includes:

  • Attendance to all theoretical lectures and hands-on sessions
  • Course materials: slides of the theoretical lectures, step-by-step protocols, useful tips & tricks, relevant literature
  • Advanced hands-on exercises
  • Trouble-shooting guidance
  • Graduation certificate

NOTE: the maximum number of registrations has been reached. You can still register and be added to the waiting list, or you can sign up to our newsletters and be informed of the next edition of this course.


We promote education above all. This is why we have 2 scholarships available to the students with fewer resources and 2 scholarships reserved to scientists impacted by armed conflicts, such as the one occurring in Ukraine. These scholarships will cover the registration fees entirely.

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

Scholarship awardees (2022):

  • Mônica Pires Gravina de Oliveira, Federal University of Rio de Janeiro
  • Ihor Arefiev, Institute of Biology and Medicine of Taras Shevchenko National University of Kyiv
  • Eric Velasco, University of Sao Paulo

Contact us