Výpis publikací

BUČEKOVÁ, Gabriela; Ondřej SCHINDLER; Tomáš SVOBODA; Adrián ROŠINEC; Tomáš RAČEK; Dominik TICHÝ a Radka SVOBODOVÁ. PDBCharges: Quantum-mechanical partial atomic charges for PDB structures. In Czech PhD Bioinformatics Conference. 2025.

SCHINDLER, Ondřej; Tomáš SVOBODA; Adrián ROŠINEC; Tomáš RAČEK; Gabriela BUČEKOVÁ; Dominik TICHÝ; Karel BERKA a Radka SVOBODOVÁ. PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures. Nucleic acids research. Oxford: Oxford University Press, 2025, s. 1-6. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaf401.

SCHINDLER, Ondřej; Karel BERKA; Alessio CANTARA; Aleš KŘENEK; Dominik TICHÝ; Tomáš RAČEK a Radka SVOBODOVÁ. αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research. Oxford: Oxford University Press, 2023, roč. 51, W1, s. "W11"-"W16", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad349.

SVOBODOVÁ, Radka; Karel BERKA; Ivana HUTAŘOVÁ VAŘEKOVÁ; Tomáš RAČEK a Ondřej SCHINDLER. New ways of protein family visualization in AlphaFold era. In 3D-BioInfo | ICSB 3D-SIG | ELIXIR Czech Republic Community Meeting in Structural Bioinformatics. 2023.

SCHINDLER, Ondřej; Tomáš RAČEK a Radka SVOBODOVÁ. Alphacharges - a web service for calculating QM-like partial atomic charges for AlphaFold proteins. In XXI. setkání biochemiků a molekulárních biologů. 2022.

RAČEK, Tomáš; Ondřej SCHINDLER; Lenka PTÁČNÍKOVÁ a Radka SVOBODOVÁ. Atomic Charge Calculator II – a web service for calculating partial atomic charges. In ENBIK2022. 2022. ISBN 978-80-7592-127-7.

SCHINDLER, Ondřej; Tomáš RAČEK a Radka SVOBODOVÁ. Prediction of QM-like partial atomic charges for alphafold. In XXII. Workshop of biophysical chemists and electrochemists. 2022. ISBN 978-80-280-0087-5.

SCHINDLER, Ondřej; Tomáš RAČEK; Kamil JELÍNEK a Radka SVOBODOVÁ. QM-like partial atomic charges for AlphaFold available online. In ENBIK2022. 2022. ISBN 978-80-7592-127-7.

RAČEK, Tomáš a Ondřej SCHINDLER. COMPUTER-AIDED MODEL DESIGN OF EMPIRICAL METHODS FOR CALCULATING PARTIAL ATOMIC CHARGES. Online. In 978-9-492-85918-1. MODELLING AND SIMULATION 2021: 35TH ANNUAL EUROPEAN SIMULATION AND MODELLING CONFERENCE 2021 (ESM 2021). GHENT: EUROSIS, 2021, s. 16-20. ISBN 978-94-92859-18-1.

SCHINDLER, Ondřej; Tomáš RAČEK; Aleksandra MARŠAVELSKI; Jaroslav KOČA; Karel BERKA a Radka SVOBODOVÁ. Optimized SQE atomic charges for peptides accessible via a web application. Journal of Cheminformatics. Chemistry Central Ltd. in association with BioMed Central, 2021, roč. 13, č. 1, s. 45-55. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-021-00528-w.

SCHINDLER, Ondřej; Tomáš RAČEK; Aleksandra MARŠAVELSKI; Radka SVOBODOVÁ a Jaroslav KOČA. Partial atomic charges for proteins. In 1st Student Conference in Structural Biology, 2021. 2021.

SCHINDLER, Ondřej; Tomáš RAČEK; Radka SVOBODOVÁ a Karel BERKA. QM-like partial atomic charges for proteins available online. In ELIXIR CZ Annual Conference 2021. 2021. ISBN 978-80-86241-67-8.

RAČEK, Tomáš; Ondřej SCHINDLER; Dominik TOUŠEK; Vladimír HORSKÝ; Karel BERKA; Jaroslav KOČA a Radka SVOBODOVÁ. Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic acids research. Oxford: Oxford University Press, 2020, roč. 48, W1, s. "W591"-"W596", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa367.

SCHINDLER, Ondřej; Tomáš RAČEK; Radka SVOBODOVÁ; Karel BERKA a Jaroslav KOČA. SQE charge calculation and its applicability for proteins. In ELIXIR CZ Annual Conference 2020. 2020. ISBN 978-80-86241-65-4.

RAČEK, Tomáš; Ondřej SCHINDLER; Vladimír HORSKÝ; Jaroslav KOČA; Dominik TOUŠEK a Radka SVOBODOVÁ VAŘEKOVÁ. AtomicChargeCalculator II. In ELIXIR CZ Annual Conference 2019. 2019. ISBN 978-80-86241-61-6.

SCHINDLER, Ondřej; Tomáš RAČEK; Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Partial atomic charges for proteins. In ELIXIR CZ Annual Conference 2019. 2019. ISBN 978-80-86241-61-6.

RAČEK, Tomáš; Ondřej SCHINDLER; Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Empirical methods for calculation of partial atomic charges – applicability for proteins? In ENBIK2018. 2018. ISBN 978-80-7592-017-1.