Structural bioinformatics
research group

Welcome to the website of the Structural bioinformatics research group. Our research group is affiliated with the National Centre for Biomolecular Research at the Faculty of Science, Masaryk University

In our research, we focus on analysing protein structures, protein fragments, and whole protein families. Specifically, we visualise, validate, and annotate protein structures, detect protein channels and fragments, and calculate the properties of proteins. In parallel, we also develop software tools for performing these analyses. Our software is integrated into key structural bioinformatics databases such as Protein Data Bank and CATH.


News

Successfully defended dissertation thesis

19th January 2024

Yesterday, on 18th January, our colleague Ondřej Schindler successfully defended his dissertation thesis at the Faculty of Science, Masaryk University. The topic of his thesis is "Partial atomic charges for proteins". 

The thesis first focuses on existing empirical methods for partial atomic charge calculation and their implementation in the Atomic Charge Calculator II web server, with some of the methods being implemented there for the first time ever. The next part of the thesis introduces the SQE+qp, an empirical method for partial atomic charge calculation with cutting-edge quality results for proteins. This advantage of the SQE+qp method is utilised in the αCharges web server presented in the final part of the thesis. Charges provides the ability to automatically protonate any protein in the AlphaFold DB and compute the protein's partial atomic charges that are useful for further research.

Congratulations, Ondřej!

ChannelsDB 2.0 was published in an article

7th December 2023

In 2018, the first version of our ChannelsDB database was published. Now, its second version was made public in the article ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era published in the Database issue of the Nucleic Acids Research journal. ChannelsDB 2.0 results from a broad cooperation between the Palacký University, the Loschmidt Laboratories, the RECETOX, the International Clinical Research Center at St. Anne's University Hospital, and our research group.

ChannelsDB 2.0 provides, as did its predecessor, structural information about the position, geometry, and physicochemical properties of protein tunnels (i.e. channels and pores). It supports input structural data not only from the Protein Data Bank but also from the popular but huge AlphaFoldDB. Aside from tunnels discovered by MOLE, the database now houses tunnels discovered by the CAVER tool. And last, but by no means least, the second version of the ChannelsDB provides tunnels that start from cofactors within the AlphaFill database. Therefore, it is no surprise that it contains approximately 4.6 times more channel annotations than the ChannelsDB 1.0.

An article was published in collaboration with PDBe

6th December 2023

Our colleague, Romana Gáborová, has recently co-authored an article with the Protein Data Bank (PDB) in Europe. The paper deals with current annotation practices (or the lack of such practices in most cases) of macromolecular complex assemblies. The authors propose a method to describe assemblies and enrich them with relevant biological context. An important benefit of the presented approach is the improvement of PDB's FAIR attributes.

The manuscript "Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data" has been published in the Scientific Data journal.

Our contribution to the 3D-Bioinfo | ICSB 3D-SIG | ELIXIR CZ conference

5th December 2023

The joint conference, named 3D-BioInfo | ICSB 3D-SIG | ELIXIR Czech Republic Community Meeting in Structural Bioinformatics, took place from 15th to 17th November 2023 in the Prague Congress Center. Our group had a nontrivial presence there with one oral presentation and six posters. The presentation about New ways of protein family visualization in AlphaFold era was given by our group leader.

Our contribution to the XXII. setkání biochemiků a molekulárních biologů

4th December 2023

The traditional Czech conference XXII. setkání biochemiků a molekulárních biologů took place from 14th to 15th November 2023 in the Hotel Continental in Brno. The event is organised by the Czech Society for Biochemistry and Molecular Biology and two departments at the Faculty of Science of Masaryk University: the Department of Biochemistry and the National Centre for Biomolecular Research.

Our group had a substantial presence at the conference, with one poster by Jana and three oral presentations. On the first day, Radka had a presentation about Analyses of biomacromolecular structures in AlphaFold era, while Tomáš R. talked to the auditorium about Management of life-science data and their metadata. Gabriela then presented her research (Investigating the rare conformation of small rings in ligands) the next day.

Dean's Award for Dominik

1st December 2023

Do you think your outstanding thesis loses all interest the moment your defence is successfully finished? Think twice! Dominik Tichý, our graduate student, was awarded the Dean's Award for his thesis. The dean of the Faculty of Informatics, Masaryk University, awards students who defend an outstanding thesis with a perfect score (i.e. their defence is evaluated with an A - excellent score).

Dominik is the fourth holder of this prestigious award among the current line-up of our research group. Congratulations!

Researcher's Night 2023

30th November 2023

The Czech European Researchers' Night is a long-time yearly event aimed at popularising the seemingly mystical world of science. Many science laboratories open their gates to the public for one night while scientists prepare interesting programmes comprised mainly of wide-audience presentations and hands-on activities for children and adults alike.

The topic of this year's Researcher's Night was Mystery. The Structural bioinformatics research group took part in this event with its stall as part of a wide programme organised by the National Centre for Biomolecular Research. At the end of the event, our on-site team was exhausted but happy with the enormous interest our stall had among the visiting public.

Our contribution to the IBERGRID 2023 conference

30th September 2023

This Thursday,  28th September, our colleague Adrián Rošinec had a presentation about his research on the 12th Iberian Grid Conference (IBERGRID 2023). The conference was held in Benasque, Spain, and spanned from 25th to Friday 29th September. 

Successfully defended dissertation thesis

12th September 2023

Last Friday, 8th September, our colleague Aliaksei Chareshneu successfully defended his dissertation thesis at the Faculty of Science, Masaryk University. The topic of his thesis is "Visualization of protein structures, complexes, and annotations". The thesis contains results across a broad field of research, from visualising cell imaging data and their integration with molecular structures through work on secondary structure consensus for protein families to creating a web database for deep diving into annotations of nicotinic acetylcholine receptors.

Congratulations, Aliaksei!

The thesis topics are online

8th August 2023

Supervisors from the Structural bioinformatics research group are offering five topics for bachelor's theses and two for master's theses. The topics are described on this website in English and in Czech.

If you are interested in a dissertation thesis topic in the research direction of the Structural Bioinformatics research group, don't hesitate to get in touch with the research group leader.

Semestral project topics

5th July 2023

Supervisors from the Structural bioinformatics research group are currently offering seven topics of projects that typically span one semester and which solution rewards students with credits. The topics are described on this website in English as well as in Czech.

If you are interested in topics of bachelor's or master's theses, heads up! Let it be known that our research group is currently working on these topics. They will be published on this website soon.

Five theses successfully defended

3rd July 2023

During the last fortnight, five of our colleagues successfully defended their thesis as the spring semester of 2023 slowly but surely ended.

Lenka Ptáčníková defended her master's thesis at the Faculty of Science, Masaryk University. Her thesis topic is "API for a web application Atomic Charge Calculator II". Lenka's work has greatly benefitted our research group since Atomic Charge Calculator II users requested an API to be implemented.

Jan Bříza defended his bachelor's thesis also at the Faculty of Science, Masaryk University. His thesis topic is trendy: "Comparison of machine-learning approaches for calculating partial atomic charges". Among other results, Jan's work has shown us that promoting reproducibility in science is still an ongoing task.

Amálie Švehlová defended her bachelor's thesis at the Faculty of Science, Masaryk University. Her thesis topic is "Vizualization of protein families using 2D diagrams". The crux of Amálie's work was analysing of quality of 2D diagrams that users encounter in our 2DProts database. Her findings will be used to elevate the quality of diagrams offered to users.

Tomáš Gabriš defended his bachelor's thesis at the Faculty of Informatics, Masaryk University. His thesis topic is: "bio.tools Sum application backend". It is another user-requested topic. Users and stakeholders of the ELIXIR pan-European project will use and benefit from Tomáš's results.

Dominik Tichý defended his bachelor's thesis also at the Faculty of Informatics, Masaryk University. His thesis topic is "Modern visualization of partial atomic charges in Mol*". Dominik looks forward to continuing his work on extending the possibilities of the best-in-class Mol* toolkit.

Congratulations to all five of our colleagues!

A preprint was published in collaboration with PDBe

3rd July 2023

Our colleague, Romana Gáborová, has recently co-authored a manuscript with the Protein Data Bank (PDB) in Europe. The manuscript deals with current annotation practices (or the lack of such practices in most cases) of macromolecular complex assemblies. The authors propose a method to describe assemblies and enrich them with relevant biological context. An important benefit of the presented approach is the improvement of PDB's FAIR attributes.

The manuscript "Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data" is available as a preprint in bioRxiv.

αCharges and Mol*VS published in 2023 NAR WSI

19th May 2023

The Web Server issue of the Nuclear Acids Research hosts two articles authored by our research group this year. The first informs about Ondřej Schindler's AlphaCharges (αCharges) web server. This application computes partial atomic charges for more than 200 million protein structures in the AlphaFoldDB database. Each on-demand calculation is completed fast using our SQE+qp empirical charge calculation method. Results can be downloaded or viewed in our Mol* viewer. The full text of the article is openly available here: αCharges: partial atomic charges for AlphaFold structures in high quality.

The second article focuses on an extension of our widely adopted Mol* viewer. David Sehnal and his team developed Mol* Volumes and Segmentations (Mol*VS), which adds support for the interactive visualisation of cellular imaging data into Mol*. All entries of the community-recognised repositories EMDB and EMPIAR are ready for visualisation in a web browser. As is David's custom, everything is fast and bandwidth-thrifty, meaning that users can view the results of electron and light microscopy experiments on their smartphones. The full text of the article is openly available here: Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations

Online advanced drug design workshop

25th January 2023

Our external associate,  Karel Berka, is organising an Advanced in silico Drug Design workshop/challenge. It will take place from 30th January to 3rd February 2023.  The workshop will cover structure-based drug design (molecular docking, molecular dynamics, structural bioinformatics tools) and ligand-based drug design (QSAR, pharmacophores, deep learning) with lectures and on-hand tutorials. The workshop is a hybrid one, with its venue being in Olomouc. More information is available on the workshop's website.

Two new doctoral students

18th January 2023

Two doctoral students have joined our research group: Adrián Rošinec and Tomáš Svoboda. They will both work on their theses under the supervision of the leader of our research group, Radka Svobodová. The thesis of Adrián is "Metadata for annotation of experimental data". Tomáš's thesis is "Bioinformatics workflow for experimental data management".

Successfully defended dissertation thesis

18th January 2023

This Monday, 16th January, our colleague David Sehnal successfully defended his dissertation thesis at the Faculty of Science, Masaryk University. The topic of his thesis is "Visualization of biomacromolecules". Perhaps the most remarkable part of his recent success is that it is David's second doctoral degree!

Congratulations, David!

Interview with group leader Radka Svobodová

4th October 2022

Our group leader recently gave an interview published on the website of CEITEC. The interview revolved around the Biological Data Management and Analysis Core Facility at CEITEC Masaryk University, where Radka has the head position. Many members of the Structural bioinformatics research group also work in the core facility.

The interview can be found here.

Two dissertation theses successfully defended

12th September 2022

On 8th September, there were two formal occasions in the National Centre for Biomolecular Research. Two doctoral students have successfully defended their theses. Vladimír Horský has defended his dissertation thesis on the topic of "Validation of molecular 3D structures", while Adam Midlik defended his dissertation thesis on the topic of "Annotation and visualization of protein secondary structure".

Our heartiest congratulations go to both successful students.

Two new undergraduate students

12th September 2022

Two undergraduate students from the Faculty of Informatics have joined our research group: Tomáš Gabriš and Dominik Tichý. They will both work on their theses under the supervision of Tomáš Raček. The thesis of Tomáš Gabriš is "Extension of the bio.tools Sum application", while Dominik's thesis is "Modern visualisation of partial atomic charges in Atomic Charge Calculator II".

Two new undergraduate students

9th August 2022

Two undergraduate students have joined our research group: Jan Bříza and Anna Punčochářová.  They will both work on their theses under the supervision of Tomáš Raček. Jan's thesis is "Comparison of machine learning approaches for the computation of partial atomic charges", while Anna's thesis is "Interface for processing of life science metadata".

First place in a conference competition

21st July 2022

On 29th June this year, the 22nd iteration of the traditional Workshop of Biophysical Chemists and Electrochemists took place at the Bohunice University Campus of the Faculty of Science, Masaryk University. This conference held a competition in the quality of presentation among young scientists. Of the eight competitors, our colleague Ondřej Schindler emerged victorious with his "Prediction of QM-like Partial Atomic Charges for AlphaFold" presentation. The abstract of his presentation is available on page 30 of the conference proceedings.

Congratulations, Ondřej!

Four theses successfully defended

21st July 2022

In June this year, four of our colleagues successfully defended their thesis.

Viktoriia Doshchenko defended her master's thesis at the Faculty of Science, Masaryk University. Her thesis topic is "Workflow for validation of ring conformation". After this accomplishment, Viktoriia decided to stay with our research group as a doctoral student. She will work on her doctoral thesis topic, "Development of workflow from protein structure analysis".

Jana Porubská and Gabriela Bučeková, our doctoral student colleagues, decided to broaden their horizons in bioinformatics. The culmination of their efforts was the successful defence of their bachelor's theses at the Faculty of Science, Masaryk University. Jana's thesis topic is "Validation of ring conformations in polycyclic molecules", while Gabriela's thesis topic is "Analysis of a relation between protein structure quality and publication sources".

The fourth of our successful colleagues is Kamil Jelínek, who defended his bachelor's thesis at the Faculty of Science, Masaryk University. His thesis topic is "Analysis of prediction quality of hydrogen atom positions in proteins".

Congratulations to all four of our colleagues: Viktoriia, Jana, Gabriela, and Kamil!

A new source of funding from GACR

20th February 2022

Last year, our colleague Dr. David Sehnal braved an application for a grant from the JUNIOR STAR programme of the Czech Science Foundation (GACR). The JUNIOR STAR programme is aimed towards young scientists whose doctoral degree is no older than eight years. Grants from this programme can support five-year projects with up to 25 million CZK.

On 2nd November 2021, GACR announced that David's grant proposal "Cell*: a web platform for visualization, modelling and dynamics of organelle- and cell-sized structures" has been accepted by the funding agency. Congratulations, David!

Successfully defended dissertation thesis

18th February 2022

On 17th February, our colleague Tomáš Raček has successfully defended his dissertation thesis at the Faculty of Informatics, Masaryk University. The topic of his thesis is "Empirical methods for calculating partial atomic charges".

Congratulations, Tomáš!

Two theses successfully defended

15th December 2021

On 3rd December, there were two formal occasions in the National Centre for Biomolecular Research. Ondřej Schindler, our doctoral student, has defended his rigorous thesis on the topic of "Partial atomic charges of peptides".

On the same day, our doctoral student Stanislav Geidl defended his doctoral thesis on the topic of "Chemoinformatical methods for prediction of physico-chemical properties of molecules".

Our heartiest congratulations go to both successful students.