RNDr. Tomáš Raček, Ph.D.

2025

• 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

  Article in Periodical

  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

• Gromacs MetaDump: a tool for extracting GROMACS simulation metadata

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

  Article in Periodical

  Journal of Cheminformatics, year: 2025, volume: 17, edition: 1, DOI

• MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update)

  RAČEK Tomáš VEĽKÝ Dušan BUČEKOVÁ Gabriela SCHINDLER Ondřej HUTAŘOVÁ VAŘEKOVÁ Ivana ŠPAČKOVÁ Anna BAZGIER Václav BERKA Karel SVOBODOVÁ Radka

  Article in Periodical

  Bioinformatics, year: 2025, volume: 41, edition: 9, DOI

• PDBCharges: Quantum-mechanical partial atomic charges for PDB structures

  BUČEKOVÁ Gabriela SCHINDLER Ondřej SVOBODA Tomáš ROŠINEC Adrián RAČEK Tomáš TICHÝ Dominik SVOBODOVÁ Radka

  Conference abstract

  Year: 2025, type: Conference abstract

• PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

  SCHINDLER Ondřej SVOBODA Tomáš ROŠINEC Adrián RAČEK Tomáš BUČEKOVÁ Gabriela TICHÝ Dominik BERKA Karel SVOBODOVÁ Radka

  Article in Periodical

  Nucleic Acids Research, year: 2025, volume: 53, edition: W1, DOI

2024

• Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0

  ŠPAČKOVÁ Anna BAZGIER Václav RAČEK Tomáš SEHNAL David SVOBODOVÁ Radka BERKA Karel

  Chapter of a book

  Protein Bioinformatics, edition: Vyd. 1, year: 2024, number of pages: 15 s.

• Data Management of Biological Imaging Data

  SVOBODA Tomáš ROŠINEC Adrián RAČEK Tomáš SVOBODOVÁ Radka

  Appeared in Conference without Proceedings

  Year: 2024, type: Appeared in Conference without Proceedings

• ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

  ŠPAČKOVÁ Anna VÁVRA Ondřej RAČEK Tomáš BAZGIER Václav SEHNAL David DAMBORSKÝ Jiří SVOBODOVÁ Radka BEDNÁŘ David BERKA Karel

  Article in Periodical

  Nucleic Acids Research, year: 2024, volume: 52, edition: D1, DOI

• Scientific Dataset Management System for the Research Institute Based on Onedata

  SVOBODA Tomáš ROŠINEC Adrián RAČEK Tomáš HANDL Josef KŘENEK Aleš SVOBODOVÁ Radka

  Conference abstract

  Year: 2024, type: Conference abstract