RNDr. Ondřej Schindler, Ph.D.

2025

• 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

2023

• New ways of protein family visualization in AlphaFold era

  SVOBODOVÁ Radka BERKA Karel HUTAŘOVÁ VAŘEKOVÁ Ivana RAČEK Tomáš SCHINDLER Ondřej

  Appeared in Conference without Proceedings

  Year: 2023, type: Appeared in Conference without Proceedings

• αCharges: partial atomic charges for AlphaFold structures in high quality

  SCHINDLER Ondřej BERKA Karel CANTARA Alessio KŘENEK Aleš TICHÝ Dominik RAČEK Tomáš SVOBODOVÁ Radka

  Article in Periodical

  Nucleic Acids Research, year: 2023, volume: 51, edition: W1, DOI

2022

• Alphacharges - a web service for calculating QM-like partial atomic charges for AlphaFold proteins

  SCHINDLER Ondřej RAČEK Tomáš SVOBODOVÁ Radka

  Appeared in Conference without Proceedings

  Year: 2022, type: Appeared in Conference without Proceedings

• Atomic Charge Calculator II – a web service for calculating partial atomic charges

  RAČEK Tomáš SCHINDLER Ondřej PTÁČNÍKOVÁ Lenka SVOBODOVÁ Radka

  Conference abstract

  Year: 2022, type: Conference abstract

• Prediction of QM-like partial atomic charges for alphafold

  SCHINDLER Ondřej RAČEK Tomáš SVOBODOVÁ Radka

  Appeared in Conference without Proceedings

  Year: 2022, type: Appeared in Conference without Proceedings