Ing. Tomáš Trnka, Ph.D.
Assistant professor, National Centre for Biomolecular Research
Total number of publications: 15
2023
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Efficient pipe interface between the Amsterdam Modeling Suite and external software
Year: 2023, type: Appeared in Conference without Proceedings
2018
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Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions
Journal of Chemical Theory and Computation, year: 2018, volume: 14, edition: 1, DOI
2017
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Different QM/MM approaches to study enzymatic reactions: ppGalNAcT2 glycosyltransferase
Year: 2017, type: Conference abstract
2016
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Bridging the Gap between QM and MM with ReaxFF: Towards Accurate Reactive Molecular Dynamics of Enzymes
Year: 2016, type: Appeared in Conference without Proceedings
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Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2
Journal of Chemical Theory and Computation, year: 2016, volume: 12, edition: 12, DOI
2015
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Catalytic Mechanism of the ppGalNAcT2 Retaining Glycosyltransferase Inferred From QM/MM Calculations
Year: 2015, type: Appeared in Conference without Proceedings
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Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
PLoS Computational Biology, year: 2015, volume: 11, edition: 4, DOI
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Towards Fast and Accurate Reactive Molecular Dynamics of Enzymes
Year: 2015, type: Appeared in Conference without Proceedings
2014
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Catalytic Mechanism of the ppGalNAcT2 Retaining Glycosyltransferase Inferred From QM/MM Calculations
Year: 2014, type: Appeared in Conference without Proceedings
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Combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2
Year: 2014, type: Conference abstract