Programme features

This 5-day course will bring together computational and experimental (bio)chemistry experts who will give comprehensive lectures on understanding and engineering enzyme catalysis. Hands-on practical sessions will be focused on how to use state-of-the-art software and webservers.
The four focus areas are:
(i) The EBI Enzyme Portal: a portal with enzyme resources, provided by the European Bioinformatics Institute (EMBL-EBI) and beyond (including the AlphaFold dataset) to be covered by Professor Dame Janet Thornton and Dr. Deepti Gupta;  (ii) Molecular dynamics simulation as a tool in protein engineering to be covered by Prof. Chris Oostenbrink; (iii) Computational tools for designing and engineering enzymes to be covered by Prof. Jiri Damborsky and Dr. David Bednář, Ph.D.  and (iv) de novo Protein Design to be covered by Prof. David Baker and Research Asst. Prof. Ajasja Ljubetič.  

The focus topics will be complemented by lectures of Professor Ita Gruić-Sovulj on kinetic analysis of enzyme-catalyzed reactions and Prof. Kenneth A. Johnson on the versatile KinTek Explorer software for simulation and data-fitting in the field of enzyme kinetics. Professor Don Hilvert covers the use of computational and experimental strategies for the design of proteins with customized catalytic properties. We will also address the QM/MM and EVB approaches to simulate enzyme-catalyzed reactions in lectures given by Dr. Marc Van der Kamp and Dr. Jernej Stare. Our program addresses the topic of allosteric pathways in protein function by Asst Prof. Tina Perica, whereas Associate Professor Per-Olof Syrén will address the topic of novel enzyme engineering strategies for applications in biopolymer science and for the generation of superior biopharmaceuticals and fine chemicals from renewable sources.

Students will be encouraged to work on their own research problems using their own laptops for working with the web-tools that will be covered in the tutorials. For some tutorials it could be required to install software on your laptop in order to be able to run a tutorial more efficiently. Please make sure that it is possible to install software on your laptop, in advance of the actual course event. Students will present and discuss their own research results during the poster session and short oral presentations. The programme will encourage interactions between students and lecturers and will provide opportunities to establish new professional relationships.

Course material will be provided via an on-line platform. At this platform, we will also have a shared document, accessible to all course participants, which can be used for asking questions related to the lectures and tutorials. The program includes two Q&A sessions covering the topics of all tutorials and lectures, respectively, on thursday afternoon. The posters will be located in the coffee area and can also be discussed between the sessions.

Program

The detailed program can be found here

Four focus topics

EBI - enzyme portal: 
Professor Dame Janet Thornton and Dr. Deepti Gupta - Enzyme Portal: a portal for enzyme resources at the European Bioinformatics Institute (EMBL-EBI) and beyond

Molecular Dynamics analysis:
Prof. Chris Oostenbrink - Analysis of protein conformational changes from molecular dynamics simulations of proteins

Rosetta/Robetta
Prof. David Baker and Research Asst. Prof. Ajasja Ljubetič - de novo protein design

Caver Web:
Prof. Jiří Damborský and Dr. David Bednář - Engineering ligand access pathways


Seven complementary lectures

Professor Ita Gruić-Sovulj - kinetic analysis of enzyme-catalyzed reactions

Prof. Kenneth A. Johnson - the versatile KinTek Explorer software for simulation and data-fitting software in the field of enzyme kinetics.

Professor Don Hilvert - the use of computational and experimental strategies for the design of proteins with customized catalytic properties.

Dr. Marc Van der Kamp - QM/MM approache to simulate enzyme-catalyzed reactions

Dr. Jernej Stare - EVB approache to simulate enzyme-catalyzed reactions

Asst Prof. Tina Perica - allosteric pathways in protein function

Associate Professor Per-Olof Syrén - novel enzyme engineering strategies for applications in biopolymer science and for the generation of superior biopharmaceuticals and fine chemicals from renewable sources. 

Student flash presentations

Accepted participants will be asked to provide presentation for a two-minute talk (max 2 slides).