Publication Records

HERREROS, David, Roy R. LEDERMAN, James M. KRIEGER, Amaya JIMÉNEZ-MORENO, Marta MARTÍNEZ, David MYŠKA, David STŘELÁK, Jiří FILIPOVIČ, Carlos O. S. SORZANO and José M. CARAZO. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. Nature Communications. 2023, vol. 14, No 1, p. 1-10. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-023-35791-y.

PETROVIČ, Filip and Jiří FILIPOVIČ. Kernel Tuning Toolkit. SoftwareX. Elsevier, 2023, vol. 22, neuveden, p. 1-6. ISSN 2352-7110. Available from: https://dx.doi.org/10.1016/j.softx.2023.101385.

VÁVRA, Ondřej, Jakub BERANEK, Jan ŠTOURAČ, Martin SURKOVSKY, Jiří FILIPOVIČ, Jiří DAMBORSKÝ, Jan MARTINOVIC and David BEDNÁŘ. pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinformatics. Oxford: Oxford University Press, 2023, vol. 39, No 8, p. 1-3. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btad443.

TØRRING, Jacob O, van Werkhoven BEN, Filip PETROVIČ, Floris-Jan WILLEMSEN, Jiří FILIPOVIČ and Anne C ELSTER. Towards a Benchmarking Suite for Kernel Tuners. Online. In 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). neuveden: IEEE, 2023, p. 724-733. ISBN 979-8-3503-1199-0. Available from: https://dx.doi.org/10.1109/IPDPSW59300.2023.00124.

STŘELÁK, David, David MYŠKA, Filip PETROVIČ, Jan POLÁK, Jaroslav OĽHA and Jiří FILIPOVIČ. Umpalumpa: a framework for efficient execution of complex image processing workloads on heterogeneous nodes. Computing. Springer, 2023, vol. 105, No 11, p. 2389-2417. ISSN 0010-485X. Available from: https://dx.doi.org/10.1007/s00607-023-01190-w.

HERREROS, David, Jakub KISKA, Erney RAMÍREZ-APORTELA, Jiří FILIPOVIČ, José María CARAZO and Carlos Oscar SORZANO. ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis. Journal of Molecular Biology. Elsevier, 2023, vol. 435, No 9, p. 1-14. ISSN 0022-2836. Available from: https://dx.doi.org/10.1016/j.jmb.2023.168088.

NĚMCOVÁ, Petra, Jana HOZZOVÁ and 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, p. 619-626. ISBN 978-1-4503-8713-2. Available from: https://dx.doi.org/10.1145/3477314.3506988.

SORZANO, Carlos, Amaya JIMÉNEZ-MORENO, David MALUENDA, Marta MARTÍNEZ, Erney RAMÍREZ-APORTELA, James KRIEGER, Roberto MELERO, Ana CUERVO, Javier CONESA, Jiří FILIPOVIČ, Pablo CONESA, Laura del CAÑO, Yunior FONSECA, Jorge Jiménez-de LA MORENA, Patricia LOSANA, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Jose Luis VILAS, Roberto MARABINI and Jose Maria CARAZO. On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy. Acta Crystallographica Section D: Structural Biology. Chester: International Union of Crystallography, 2022, vol. 78, No 4, p. 410-423. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798322001978.

TRAPL, Dalibor, MArtin KRUPIČKA, Vladimír VIŠŇOVSKÝ, Jana HOZZOVÁ, Jaroslav OĽHA, Aleš KŘENEK and 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, vol. 62, No 3, p. 567-576. ISSN 1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.1c00651.

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

STŘELÁK, David, Amaya JIMÉNEZ-MORENO, José VILAS, Erney RAMÍREZ-APORTELA, Ruben SÁNCHEZ-GARCÍA, David MALUENDA, Javier VARGAS, David HERREROS, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, Jan HORÁČEK, David MYŠKA, Martin HORÁČEK, Pablo CONESA, Yunior FONSECA-REYNA, Jorge JIMÉNEZ, Marta MARTÍNEZ, Mohamad HARASTANI, Slavica JONIĆ, Jiří FILIPOVIČ, Roberto MARABINI, José CARAZO and Carlos SORZANO. Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion. Molecules. Mayer und Muller, 2021, vol. 26, No 20, p. 1-14. ISSN 1420-3049. Available from: https://dx.doi.org/10.3390/molecules26206224.

HERREROS, David, Roy R LEDERMAN, James KRIEGER, Amaya JIMENEZ-MORENO, Marta MARTINEZ, David MYŠKA, David STŘELÁK, Jiří FILIPOVIČ, Ivet BAHAR, Jose Maria CARAZO and Carlos Oscar S SANCHEZ. Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials. International Union of Crystallography Journals. online, 2021, vol. 8, No 6, p. 992-1005. ISSN 2052-2525. Available from: https://dx.doi.org/10.1107/S2052252521008903.

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

DAMBORSKÝ, Jiří, David BEDNÁŘ, Zbyněk PROKOP, Martin MAREK, Stanislav MAZURENKO, Jan ŠTOURAČ, Sérgio Manuel MARQUES, Gabriela Filipa FONSECA PINTO, Joan PLANAS IGLESIAS, Miloš MUSIL, Jiří HON, Ondřej VÁVRA, Rayyan Tariq KHAN, Jiří FILIPOVIČ and Barbora KOZLÍKOVÁ. Computational enzyme design for metabolic engineering. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

JIMÉNEZ-MORENO, Amaya, David STŘELÁK, Jiří FILIPOVIČ, José María CARAZO and Carlos Óscar S. SORZANO. DeepAlign, a 3D Alignment Method based on Regionalized Deep Learning for Cryo-EM. Journal of Structural Biology. San Diego,USA: Academic Press, 2021, vol. 213, No 2, p. "107712", 14 pp. ISSN 1047-8477. Available from: https://dx.doi.org/10.1016/j.jsb.2021.107712.

S. SORZANO, Carlos Oscar, Amaya JIMÉNEZ-MORENO, David MALUENDA, Erney RAMÍREZ-APORTELA, Marta MARTÍNEZ, Ana CUERVO, Roberto MELERO, Jose Javier CONESA, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK, Jiří FILIPOVIČ, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Pablo CONESA, Laura DEL CAÑO, Yunior FONSECA, Jorge JIMÉNEZ DE LA MORENA, Jose Ramon MACÍAS, Patricia LOSANA, Roberto MARABINI and Jose-Maria CARAZO. Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods. In Structural Proteomics. Clifton, N.J.: Springer US, 2021, p. 257-289. Methods in Molecular Biology. ISBN 978-1-0716-1405-1. Available from: https://dx.doi.org/10.1007/978-1-0716-1406-8_13.

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

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Sérgio Manuel MARQUES, Jiří FILIPOVIČ, David BEDNÁŘ and Jiří DAMBORSKÝ. Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2021, vol. 19, May, p. 3187-3197. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2021.05.043.

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

HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ and 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, p. 105-124. Methods in Molecular Biology, vol 2266. ISBN 978-1-0716-1208-8. Available from: https://dx.doi.org/10.1007/978-1-0716-1209-5_6.

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

PETROVIČ, Filip, David STŘELÁK, Jana HOZZOVÁ, Jaroslav OĽHA, Richard TREMBECKÝ, Siegfried BENKNER and 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, vol. 108, July, p. 161-177. ISSN 0167-739X. Available from: https://dx.doi.org/10.1016/j.future.2020.02.069.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Los Alamitos: IEEE Computer Society, 2020, vol. 17, No 5, p. 1625-1638. ISSN 1545-5963. Available from: https://dx.doi.org/10.1109/TCBB.2019.2907492.

OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK and Jiří FILIPOVIČ. Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE. HOBOKEN: WILEY, 2020, vol. 32, No 21, p. 1-15. ISSN 1532-0626. Available from: https://dx.doi.org/10.1002/cpe.5962.

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

STŘELÁK, David, Jiří FILIPOVIČ, Amaya JIMÉNEZ-MORENO, Jose María CARAZO and Carlos Óscar SÁNCHEZ SORZANO. FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy. Electronics. Switzerland: MDPI, 2020, vol. 9, No 6, p. 1-25. ISSN 2079-9292. Available from: https://dx.doi.org/10.3390/electronics9061040.

STŘELÁK, David, Carlos Óscar S. SORZANO, José María CARAZO and Jiří FILIPOVIČ. A GPU acceleration of 3-D Fourier reconstruction in cryo-EM. The International Journal of High Performance Computing Applications. SAGE Publishing, 2019, vol. 33, No 5, p. 948-959. ISSN 1094-3420. Available from: https://dx.doi.org/10.1177/1094342019832958.

ŠTOURAČ, Jan, O. VAVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, Gabriela Filipa FONSECA PINTO, Andrea SCHENKMAYEROVÁ, Jiří DAMBORSKÝ and David BEDNÁŘ. Caver web: identification of tunnels and channels in proteins and analysis of ligand transport. In European Biotechnology Congress. 2019. ISSN 0168-1656. Available from: https://dx.doi.org/10.1016/j.jbiotec.2019.05.251.

ŠTOURAČ, Jan, Ondřej VÁVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Jan BREZOVSKÝ, Jiří DAMBORSKÝ and David BEDNÁŘ. Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic acids research. Oxford: Oxford University Press, 2019, vol. 47, W1, p. 414-422. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz378.

VÁVRA, Ondřej, Jiří FILIPOVIČ, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Jan ŠTOURAČ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics. Oxford: Oxford University Press, 2019, vol. 35, No 23, p. 4986-4993. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz386.

OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK and 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, p. 295-307. ISBN 978-3-030-48339-5. Available from: https://dx.doi.org/10.1007/978-3-030-48340-1_23.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Jiří FILIPOVIČ, Jan ŠTOURAČ, David BEDNÁŘ and Jiří DAMBORSKÝ. Fast Screening of Inhibitor Binding/Unbinding using Novel Software Tool CaverDock. FRONTIERS IN CHEMISTRY. LAUSANNE: FRONTIERS MEDIA SA, 2019, vol. 7, OCT 29 2019, p. 1-14. ISSN 2296-2646. Available from: https://dx.doi.org/10.3389/fchem.2019.00709.

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

STŘELÁK, David and Jiří FILIPOVIČ. cuFFTAdvisor. 2018.

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

STŘELÁK, David and Jiří FILIPOVIČ. Performance analysis and autotuning setup of the cuFFT library. Online. In ACM International Conference Proceeding Series. Limassol, Cyprus: ACM, 2018, p. nestránkováno, 6 pp. ISBN 978-1-4503-6591-8. Available from: https://dx.doi.org/10.1145/3295816.3295817.

FILIPOVIČ, Jiří, Filip PETROVIČ and Siegfried BENKNER. Autotuning of OpenCL Kernels with Global Optimizations. Online. In 1st Workshop on Autotuning and Adaptivity Approaches for Energy Efficient HPC Systems (ANDARE'2017). Portland (USA): ACM, 2017, p. nestránkováno, 6 pp. ISBN 978-1-4503-5363-2. Available from: https://dx.doi.org/10.1145/3152821.3152877.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock 1.0. 2017.

PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK and 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, vol. 146, No 11, p. "115101:1"-"115101:8", 8 pp. ISSN 0021-9606. Available from: https://dx.doi.org/10.1063/1.4978296.

FILIPOVIČ, Jiří, Jana PAZÚRIKOVÁ, Aleš KŘENEK and 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, p. 278-280. ISBN 978-90-77381-95-3.

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

PAZÚRIKOVÁ, Jana, Aleš KŘENEK and 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, p. 267-274. ISBN 978-90-77381-95-3.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ, Aleš KŘENEK, Jana PAZÚRIKOVÁ, Stanislav GEIDL and 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 and Jaroslav KOČA. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2016, vol. 8, October, p. nestránkováno, 14 pp. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-016-0171-1.

PAZÚRIKOVÁ, Jana, Tomáš RAČEK, Stanislav GEIDL, Radka SVOBODOVÁ VAŘEKOVÁ and Aleš KŘENEK. Parametrizace ekvalizace elektronegativity metodou diferenciální evoluce (Parametrization of Electronegativity Equalization Method through Differential Evolution). In ENBIK 2016. 2016.

FILIPOVIČ, Jiří, Jan PLHÁK and David STŘELÁK. Acceleration of dRMSD Calculation and Efficient Usage of GPU Caches. In Waleed Smari. Proceedings of IEEE International Conference on High Performance Computing & Simulation. neuveden: IEEE, 2015, p. 47-54. ISBN 978-1-4673-7812-3. Available from: https://dx.doi.org/10.1109/HPCSim.2015.7237020.

KŘENEK, Aleš, Karel KUBÍČEK, Richard ŠTEFL and Jiří FILIPOVIČ. Accurate Fitting SAXS Curves with NMR Structure Ensembles. Online. In Simon Lin, Vicky Huang. Proceedings of International Symposium on Grids and Clouds 2015. Pissa: Proceedings of Science, 2015, p. nestránkováno, 9 pp. ISSN 1824-8039.

SPIWOK, Vojtěch, Pavel OBORSKÝ, Jana PAZÚRIKOVÁ, Aleš KŘENEK and 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, vol. 142, No 11, p. nestránkováno, 8 pp. ISSN 0021-9606. Available from: https://dx.doi.org/10.1063/1.4914828.

FILIPOVIČ, Jiří and Siegfried BENKNER. OpenCL Kernel Fusion for GPU, Xeon Phi and CPU. In Proceedings of IEEE International Symposium on Computer Architecture and High Performance Computing. Florianópolis: IEEE, 2015, p. 98-105. ISSN 1550-6533. Available from: https://dx.doi.org/10.1109/SBAC-PAD.2015.29.

FILIPOVIČ, Jiří, Matúš MADZIN, Jan FOUSEK and Luděk MATYSKA. Optimizing CUDA code by kernel fusion: application on BLAS. The Journal of Supercomputing. Springer US, 2015, vol. 71, No 10, p. 3934-3957. ISSN 0920-8542. Available from: https://dx.doi.org/10.1007/s11227-015-1483-z.

PAZÚRIKOVÁ, Jana and 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, p. 101-111. ISBN 978-80-214-5022-6.

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

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