RNDr. Tomáš Raček, Ph.D.

Deputy Head of Core Facility, Biological Data Management and Analysis Core Facility

office: bldg. C04/234
Kamenice 753/5
625 00 Brno

e‑mail:

social and academic networks:

Basic information

Supervision

Qualifications

Publications

Type

Total number of publications: 56

2026

Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach

BUČEKOVÁ Gabriela DOSHCHENKO Viktoriia SVOBODA Tomáš PORUBSKÁ Jana CHARESHNEU Aliaksei RAČEK Tomáš HORSKÝ Vladimír SVOBODOVÁ Radka SCHINDLER Ondřej

Peer-reviewed scientific article

Journal of Cheminformatics, year: 2026, volume: 18, edition: 1, DOI
Atomic Charge Calculator III: a modern platform for calculating partial atomic charges

RAČEK Tomáš PILÁT Martin SCHINDLER Ondřej BUČEKOVÁ Gabriela TICHÝ Dominik BERKA Karel SVOBODOVÁ Radka

Peer-reviewed scientific article

Nucleic Acids Research, year: 2026, volume: 54, edition: W1, DOI
bio.tools: an expanded web service for research software in the life sciences

MENDES Ana I S IENASESCU Hans ANDERSEN Christian A T CALHOUN Erin CHMURA Piotr J COLLIER Keiler GOGA Iosif GUSTAFSSON Ove J R KALAŠ Matúš KIERKEGAARD Mads NIELSEN Niclas K JAANISO Erik JENSEN Jennifer R B LUDL Adriaan-Alexander MÉNAGER Hervé PALMBLAD Magnus MAGYAR Zsófia RAČEK Tomáš ROŠINEC Adrián RUSZ Filip STEEGHS-TURCHINA Mariia SZMIGIEL Aleksandra SVOBODOVÁ Radka SCHWÄMMLE Veit

Peer-reviewed scientific article

Nucleic Acids Research, year: 2026, volume: 54, edition: W1, DOI
GROMACS MetaDump: A tool to describe molecular dynamics simulations with powerful metadata

SLANINÁKOVÁ Terézia ROŠINEC Adrián PAVLÍK Tomáš RANDIAK Róbert SVOBODA Tomáš RAČEK Tomáš BUČEKOVÁ Gabriela SCHINDLER Ondřej ANTOL Matej KŘENEK Aleš BERKA Karel SVOBODOVÁ Radka

Conference abstract

Year: 2026, type: Conference abstract
GROMACS MetaDump: Automatic FAIR-Ready Metadata Extraction for Molecular Dynamics Simulations

ROŠINEC Adrián ČILLÍK Jakub SLANINÁKOVÁ Terézia PAVLÍK Tomáš RANDIAK Róbert SVOBODA Tomáš RAČEK Tomáš BUČEKOVÁ Gabriela SCHINDLER Ondřej ANTOL Matej KŘENEK Aleš BERKA Karel SVOBODOVÁ Radka

Appeared in Conference without Proceedings

Year: 2026, type: Appeared in Conference without Proceedings
PROPTIMUS LIVE: local constrained α-carbon optimization of proteins

SVOBODA Tomáš MIKUŠ Michal BOHUŠ Lukáš RAČEK Tomáš BUČEKOVÁ Gabriela TICHÝ Dominik BERKA Karel SVOBODOVÁ Radka SCHINDLER Ondřej

Peer-reviewed scientific article

Nucleic Acids Research, year: 2026, volume: 54, edition: W1, DOI

2025

From Gametophytes to Sporophytes: Investigating Plant Motif Distribution with GOLEM

NEVOSÁD Lukáš KLODOVÁ Božena RUDOLF Jiří RAČEK Tomáš PŘEROVSKÁ Tereza KUSOVÁ Alžbeta SVOBODOVÁ Radka HONYS David PROCHÁZKOVÁ SCHRUMPFOVÁ Petra

Conference abstract

Year: 2025, type: Conference abstract
GOLEM: A Tool for Visualizing the Distribution of Gene Regulatory Elements in Plant Promoters

NEVOSÁD Lukáš KLODOVÁ Božena RUDOLF Jiří RAČEK Tomáš PŘEROVSKÁ Tereza KUSOVÁ Alžbeta SVOBODOVÁ Radka HONYS David PROCHÁZKOVÁ SCHRUMPFOVÁ Petra

Conference abstract

Year: 2025, type: Conference abstract
GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte

NEVOSÁD Lukáš KLODOVÁ Božena RUDOLF Jiří RAČEK Tomáš PŘEROVSKÁ Tereza KUSOVÁ Alžbeta SVOBODOVÁ Radka HONYS David PROCHÁZKOVÁ SCHRUMPFOVÁ Petra

Peer-reviewed scientific article

Plant Journal, year: 2025, volume: 121, edition: 5, DOI
GROMACS MetaDump

ROŠINEC Adrián SLANINÁKOVÁ Terézia PAVLÍK Tomáš RANDIAK Róbert SVOBODA Tomáš RAČEK Tomáš BUČEKOVÁ Gabriela SCHINDLER Ondřej ANTOL Matej KŘENEK Aleš BERKA Karel SVOBODOVÁ Radka

Software

Year: 2025

Projects

Teaching