Výpis publikací

OĽHA, Jaroslav; Jana HOZZOVÁ; Matej ANTOL a Jiří FILIPOVIČ. Estimating resource budgets to ensure autotuning efficiency. PARALLEL COMPUTING. NETHERLANDS: ELSEVIER, 2025, roč. 2025, č. 123, s. 1-15. ISSN 0167-8191. Dostupné z: https://doi.org/10.1016/j.parco.2025.103126.

HOZZOVÁ, Jana; Jacob O TORRING; van Werkhoven BEN; David STŘELÁK a Richard VUDUC. FAIR Sharing of Data in Autotuning Research (Vision Paper). Online. In COMPANION OF THE 15TH ACM/SPEC INTERNATIONAL CONFERENCE ON PERFORMANCE ENGINEERING, ICPE COMPANION 2024. NEW YORK: ASSOC COMPUTING MACHINERY, 2024, s. 21-27. ISBN 979-8-4007-0445-1. Dostupné z: https://doi.org/10.1145/3629527.3651429.

NĚMCOVÁ, Petra; Jana HOZZOVÁ a Jiří FILIPOVIČ. Improving ligand transport trajectory within flexible receptor in CaverDock. Online. In SAC '22: Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing. USA: Association for Computing Machinery, 2022, s. 619-626. ISBN 978-1-4503-8713-2. Dostupné z: https://doi.org/10.1145/3477314.3506988.

TRAPL, Dalibor; MArtin KRUPIČKA; Vladimír VIŠŇOVSKÝ; Jana HOZZOVÁ; Jaroslav OĽHA; Aleš KŘENEK a Vojtěch SPIWOK. Property Map Collective Variable as a Useful Tool for a Force Field Correction. Journal of Chemical Information and Modeling. American Chemical Society, 2022, roč. 62, č. 3, s. 567-576. ISSN 1549-9596. Dostupné z: https://doi.org/10.1021/acs.jcim.1c00651.

FILIPOVIČ, Jiří; Jana HOZZOVÁ; Amin NEZARAT; Jaroslav OĽHA a Filip PETROVIČ. Using hardware performance counters to speed up autotuning convergence on GPUs. Journal of Parallel and Distributed Computing. Elsevier, 2022, roč. 160, February, s. 16-35. ISSN 0743-7315. Dostupné z: https://doi.org/10.1016/j.jpdc.2021.10.003.

VIŠŇOVSKÝ, Vladimír; Viktória SPIŠAKOVÁ; Jana HOZZOVÁ; Jaroslav OĽHA; Dalibor TRAPL; Vojtěch SPIWOK; Lukáš HEJTMÁNEK a Aleš KŘENEK. Complex simulation workflows in containerized high-performance environment. In Armenia S., Geril P. Proc. ESM 2021. Brusel: EUROSIS, 2021, s. 42-45. ISBN 978-94-92859-18-1.

PETROVIČ, Filip; Jiří FILIPOVIČ; David STŘELÁK; Jana HOZZOVÁ a Richard TREMBECKÝ. Kernel Tuning Toolkit 2.0. 2021.

HOZZOVÁ, Jana; Jiří FILIPOVIČ; Amin NEZARAT; Jaroslav OĽHA a Filip PETROVIČ. Searching CUDA code autotuning spaces with hardware performance counters: data from benchmarks running on various GPU architectures. Data in Brief. Elsevier, 2021, roč. 39, December, s. 1-12. ISSN 2352-3409. Dostupné z: https://doi.org/10.1016/j.dib.2021.107631.

HOZZOVÁ, Jana; Ondřej VÁVRA; David BEDNÁŘ a Jiří FILIPOVIČ. Simulation of Ligand Transport in Receptors Using CaverDock. In Flavio Ballante. Protein-Ligand Interactions and Drug Design. New York: Humana, New York, NY, 2021, s. 105-124. Methods in Molecular Biology, vol 2266. ISBN 978-1-0716-1208-8. Dostupné z: https://doi.org/10.1007/978-1-0716-1209-5_6.

BRÁZDIL, Tomáš; David PORTEŠ; Jiří FILIPOVIČ; Jana HOZZOVÁ; Thomas EVANGELIDIS a Konstantinos TRIPSIANES. 4D-GRAPHS. 2021.

PETROVIČ, Filip; David STŘELÁK; Jana HOZZOVÁ; Jaroslav OĽHA; Richard TREMBECKÝ; Siegfried BENKNER a Jiří FILIPOVIČ. A benchmark set of highly-efficient CUDA and OpenCL kernels and its dynamic autotuning with Kernel Tuning Toolkit. Future Generation Computer Systems. Elsevier, 2020, roč. 108, July, s. 161-177. ISSN 0167-739X. Dostupné z: https://doi.org/10.1016/j.future.2020.02.069.

OĽHA, Jaroslav; Jana HOZZOVÁ; Jan FOUSEK a Jiří FILIPOVIČ. Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE. HOBOKEN: WILEY, 2020, roč. 32, č. 21, s. 1-15. ISSN 1532-0626. Dostupné z: https://doi.org/10.1002/cpe.5962.

KŘENEK, Aleš; Jana HOZZOVÁ; Jaroslav OĽHA; Dalibor TRAPL a Vojtěch SPIWOK. Exploring Protein Folding Space with Neural Network Guided Simulations. In Alexandre Nketsa. MODELLING AND SIMULATION 2020. Brusel: EUROSIS-ETI, 2020, s. 305-309. ISBN 978-94-92859-12-9.

OĽHA, Jaroslav; Jana HOZZOVÁ; Jan FOUSEK a Jiří FILIPOVIČ. Exploiting historical data: pruning autotuning spaces and estimating the number of tuning steps. In Ulrich Schwardmann, Christian Boehme, Dora B. Heras, Valeria Cardellini, Emmanuel Jeannot, Antonio Salis, Claudio Schifanella, Ravi Reddy Manumachu, Dieter Schwamborn, Laura Ricci, Oh Sangyoon, Thomas Gruber, Laura Antonelli, Stephen L. Scott. Lecture Notes in Computer Science. Cham, Switzerland: Springer, Cham, 2019, s. 295-307. ISBN 978-3-030-48339-5. Dostupné z: https://doi.org/10.1007/978-3-030-48340-1_23.

PAZÚRIKOVÁ, Jana; Jaroslav OĽHA; Aleš KŘENEK a Vojtěch SPIWOK. Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations. arXiv, 2018, 22 s. arXiv:1801.02362.

PETROVIČ, Filip; Jiří FILIPOVIČ; David STŘELÁK a Jana PAZÚRIKOVÁ. Kernel Tuning Toolkit. 2018.

PAZÚRIKOVÁ, Jana; Aleš KŘENEK; Vojtěch SPIWOK a Mária ŠIMKOVÁ. Reducing the number of mean-square deviation calculations with floating close structure in metadynamics. Journal of Chemical Physics. Melville: American Institute of Physics, 2017, roč. 146, č. 11, s. "115101:1"-"115101:8", 8 s. ISSN 0021-9606. Dostupné z: https://doi.org/10.1063/1.4978296.

FILIPOVIČ, Jiří; Jana PAZÚRIKOVÁ; Aleš KŘENEK a Vojtěch SPIWOK. Accelerated RMSD Calculation for Molecular Metadynamics. In José Évora-Gómez and José Juan Hernandéz-Cabrera. Proceedings of the 2016 European Simulation and Modelling Conference. Ghent, Belgie: EUROSIS - ETI, 2016, s. 278-280. ISBN 978-90-77381-95-3.

KŘENEK, Aleš; Tomáš RAČEK a Jana PAZÚRIKOVÁ. Direct SAXS Curve Fitting with an Ensable of Conformations. In Molecular Machines 2016. 2016.

PAZÚRIKOVÁ, Jana; Aleš KŘENEK a Luděk MATYSKA. Guided Optimization Method for Fast and Accurate Atomic Charges Computation. In José Évora-Gómez and José Juan Hernandéz-Cabrera. Proceedings of the 2016 European Simulation and Modelling Conference. Ghent, Belgicko: EUROSIS - ETI, 2016, s. 267-274. ISBN 978-90-77381-95-3.

RAČEK, Tomáš; Radka SVOBODOVÁ VAŘEKOVÁ; Aleš KŘENEK; Jana PAZÚRIKOVÁ; Stanislav GEIDL a Jaroslav KOČA. NEEMP – nástroj pro parametrizaci EEM. In ENBIK2016. 2016. ISBN 978-80-7080-960-0.

RAČEK, Tomáš; Jana PAZÚRIKOVÁ; Radka SVOBODOVÁ VAŘEKOVÁ; Stanislav GEIDL; Aleš KŘENEK; Francesco Luca FALGINELLA; Vladimír HORSKÝ; Václav HEJRET a Jaroslav KOČA. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2016, roč. 8, October, s. nestránkováno, 14 s. ISSN 1758-2946. Dostupné z: https://doi.org/10.1186/s13321-016-0171-1.

PAZÚRIKOVÁ, Jana; Tomáš RAČEK; Stanislav GEIDL; Radka SVOBODOVÁ VAŘEKOVÁ a Aleš KŘENEK. Parametrizace ekvalizace elektronegativity metodou diferenciální evoluce. In ENBIK 2016. 2016.

SPIWOK, Vojtěch; Pavel OBORSKÝ; Jana PAZÚRIKOVÁ; Aleš KŘENEK a Blanka KRÁLOVÁ. Nonlinear vs. linear biasing in Trp-cage folding simulations. Journal of the chemical society. Faraday transactions II, Journal of chemical physics. London: Chemical society, 2015, roč. 142, č. 11, s. nestránkováno, 8 s. ISSN 0021-9606. Dostupné z: https://doi.org/10.1063/1.4914828.

PAZÚRIKOVÁ, Jana a Luděk MATYSKA. Convergence of Parareal Algorithm Applied on Molecular Dynamics Simulations. In Petr Hliněný, Zdeněk Dvořák, Jiří Jaroš, Jan Kofroň, Jan Kořenek, Petr Matula, Karel Pala. MEMICS 2014. Brno: NOVPRESS, 2014, s. 101-111. ISBN 978-80-214-5022-6.

PAZÚRIKOVÁ, Jana a Luděk MATYSKA. Electrostatics' calculation parallel in time. In CECAM workshop on Fast Methods for Long Range Interactions in Complex Particle Systems. 2013.

PAZÚRIKOVÁ, Jana a Luděk MATYSKA. Parallel methods for calculation of long-range electrostatic interactions. arXiv, 2013, 18 s.