NCBR seminar

NCBR PhD Info Day 

The attendance is mandatory for all 1st to 4th-year PhD candidates enrolled in the following programmes: Life Sciences, Biomolecular Chemistry and Bioinformatics, and Genomics and Proteomics.

NCBR seminar

Introductory lesson

Introduction of new students, program of the seminar, its rules and objectives, Introdduction of new students

NCBR Seminar

doc. Mgr. Karel Kubíček, PhD. - Interaction with G4 - (not only) structural biology approach

NCBR seminar

prof. Mgr. Lukáš Žídek, Ph.D. -Presentation of scientific data

NCBR seminar

Mgr. Jan Přibyl, Ph.D.- Mechanobiology studied using atomic force microscopy, from molecules to the cell clusters.

NCBR seminar

doc. Mgr. Jan Havliš, Dr. - Philosophy of science

NCBR seminar

doc. RNDr. Karel Berka, Ph.D.

Impact of AlphaFold to Structural Biology – What is next in AlphaFoldology

Demis Hassabis and John M. Jumper, the authors of the protein structure prediction program AlphaFold, were recently awarded the Nobel Prize in Chemistry.
In the seminar, we will briefly discuss the basis of their success and the evolution of the AlphaFold algorithm and broadly discuss what can happen now when we have reliable protein structural prediction.

NCBR Seminar

RNDr. Matej Antol, Ph.D.

AlphaFind: discover structure similarity across the proteome

NCBR seminar

Program cancelled: 

prof. Vladimír Sklenář memorial

NCBR seminar

doc. RNDr. Radka Svobodová, Ph.D. : " What we can learn from protein 3D structures"

NCBR Seminar

Mgr. Ing. Tomáš Svoboda : "Bioinformatics workflows for management of experimental data" - presentations of PhD students

Abstract:
Currently, extensive experimental data are being produced in the field of structural biology, as well as in life science in general. These data contain valuable information for the scientific community. However, their acquisition is often very time-consuming and expensive. The data are often quite complicated (differently structured file hierarchies and dependencies between them) and very large. An increasingly common and mandatory requirement of the scientific community in the future is to make data available according to FAIR principles. It is essential to structure, annotate, and archive these data appropriately to make them accessible to the community, transparently searchable, stored in standard formats, and thus reusable. The presentation will address the development of automated workflows for appropriate research data management.

NCBR seminar

NCBR Christmas assembly - a brief celebratory drink and discussions not only about the achievements and challenges of 2024.

NCBR seminar

Martin Pačesa- "Engineering complexity and function using computational protein design"

Martin Pačesa is a postdoctoral fellow at EPFL in Switzerland. He completed his PhD in Biomolecular Structure and Mechanism at the University of Zurich and previously studied at Masaryk University in Brno. His research focuses on computational protein design using artificial intelligence. He uses state-of-the-art techniques such as CRISPR, cryo-electron microscopy and X-ray crystallography.

Abstract:

Computational protein design is emerging as a powerful tool to create enzymes with novel or enhanced functionalities that cannot be achieved using traditional methods, such as rational engineering and directed evolution. However, most designed proteins to date are composed of structurally simple topologies, far from the complexity sampled in nature. To overcome this limitation, we developed a deep learning-based pipeline leveraging the incredible accuracy of AlphaFold2 for the design of proteins with complex natural protein topologies and high experimental success rates. We applied our approach to the design of soluble analogues of membrane proteins, such as GPCRs and claudins. We demonstrate that our soluble analogues are highly stable, structurally accurate, and are able to support native epitopes for antibody or G-protein binding in solution. We then extended the capabilities of our pipeline to the design of highly specific protein binders. We are now able to design binders with unprecedented experimental success rates against therapeutically relevant targets, such as PD-L1 or CD45, as well as much more challenging targets, such as CRISPR-Cas nucleases, Argonautes, and common allergens. These advancements pave the way for the accurate design of proteins with complex functions and potential applications in research, biotechnology, and therapies.

NCBR Seminar

Mgr. Viktoriia Doshchenko and Mgr.Adrián Rošinec - presentations of PhD students

Mgr. Viktoriia Doshchenko: Development of workflows for the validation of protein structures

Abstarct: Accurate validation of molecular structures is essential for ensuring the quality and reliability of data in structural biology. While existing validation tools provide critical insights into ligand properties such as bond lengths and torsion angles, ring conformations remain insufficiently explored. Rings play a vital role in molecular interactions, and the lack of systematic validation introduces potential errors in structural analysis.

The presentation addresses this gap by introducing an automated workflow for identifying and classifying ring conformations in the PDB. The workflow is paired with a user-friendly visualization tool, enabling scalable and reproducible analysis. This approach provides valuable insights into ring geometries and their implications in structural biology.

Mgr. Adrián Rošinec: Molecular dynamics data, annotations, and searching structures

Abstract: Wouldn't it be useful to quickly retrieve information about the dynamical properties, conformations, and chemical characteristics of a protein, or determine whether a structure has been part of existing MD simulations? The aim of my PhD project is to design a database for MD simulations, ensuring proper annotation and integration with existing resources such as PDB. This includes developing tools, based on AlphaFind, to enable highly efficient searches within these large MD data.