Tomáš Raček

Central European Institute of Technology — Czech Republic

Materials Science · Physical Sciences

24h-index2.1kcitations103works0.72yr avg
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Research Topics

Machine Learning in Materials Science(12), X-ray Diffraction in Crystallography(10), Geochemistry and Geologic Mapping(9), Protein Structure and Dynamics(8), Scientific Computing and Data Management(8)

Publications103 total

GROMACS MetaDump: A tool to describe molecular dynamics simulations with powerful metadata
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
GROMACS MetaDump: A tool to describe molecular dynamics simulations with powerful metadata
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach
Journal of Cheminformatics·2026Open Access
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata
Journal of Cheminformatics·2025Open Access
MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update)
Bioinformatics·2025· 1 citedOpen Access
PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures
Nucleic Acids Research·2025· 1 citedOpen Access
<scp>GOLEM</scp> : A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte
The Plant Journal·2025· 4 citedOpen Access
RBP-Tar – a searchable database for experimental RBP binding sites
F1000Research·2024· 1 citedOpen Access
RBP-Tar – a searchable database for experimental RBP binding sites
F1000Research·2024Open Access
GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte
2024Open Access
Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0
Methods in molecular biology·2024· 1 cited
Transcriptional profiling upon T cell stimulation reveals down-regulation of inflammatory pathways in T and B cells in SLE versus Sjögren’s syndrome
npj Systems Biology and Applications·2023· 4 citedOpen Access
Onedata4Sci: Life science data management solution based on Onedata
arXiv (Cornell University)·2023· 3 citedOpen Access
GOLEM: distribution of Gene regulatOry eLEMents within the plant promoters
arXiv (Cornell University)·2023Open Access
ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era
Nucleic Acids Research·2023· 17 citedOpen Access
Analysis and Visualization of Protein Channels, Tunnels and Pores with MOLEonline &amp;amp; ChannelsDB 2.0
2023Open Access
ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era
2023Open Access
RBP-Tar – a searchable database for experimental RBP binding sites
F1000Research·2023· 1 citedOpen Access
αCharges: partial atomic charges for AlphaFold structures in high quality
Nucleic Acids Research·2023· 3 citedOpen Access
An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems
2023· 2 citedOpen Access
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Frequent Co-authors

Radka Svobodová Vařeková(15), Christoph Klein(11), Jacek Puchałka(11), Brigitte M. Pützer(7), Karel Berka(6), Jaroslav Koča(6), Aleš Křenek(6), Ehsan Bahrami(5), Alejandro A. Schäffer(5), Ondřej Schindler(5), Daniel Kotlarz(4), Maximilian Witzel(4), Heinrich Schmidt(4), Nima Rezaei(3), Gordon Peters(3), Jutte van der Werff ten Bosch(3), Päivi M. Järvinen(3), E. Michael Gertz(3), Dietmar Pfeifer(3), Michael H. Albert(3)