| A benchmark set of highly-efficient CUDA and OpenCL kernels and its dynamic autotuning with Kernel Tuning Toolkit F Petrovič, D Střelák, J Hozzová, J Ol’ha, R Trembecký, S Benkner, ... Future Generation Computer Systems 108, 161-177, 2020 | 54 | 2020 |
| Using hardware performance counters to speed up autotuning convergence on GPUs J Filipovič, J Hozzová, A Nezarat, J Ol'ha, F Petrovič Journal of Parallel and Distributed Computing 160, 16-35, 2022 | 20 | 2022 |
| Nonlinear vs. linear biasing in Trp-cage folding simulations V Spiwok, P Oborský, J Pazúriková, A Křenek, B Králová The Journal of chemical physics 142 (11), 115101, 2015 | 15 | 2015 |
| NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges T Raček, J Pazúriková, RS Vařeková, S Geidl, A Křenek, FL Falginella, ... Journal of Cheminformatics 8 (1), 57, 2016 | 14 | 2016 |
| Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps J Oľha, J Hozzová, J Fousek, J Filipovič Concurrency and Computation: Practice and Experience 32 (21), e5962, 2020 | 8 | 2020 |
| Guided Optimization Method for Fast and Accurate Atomic Charges Computation J PAZÚRIKOVÁ, A Křenek, L Matyska European Simulation and Modelling Conference, 267-274, 2016 | 8 | 2016 |
| Kernel tuning toolkit F Petrovič, J Filipovič SoftwareX 22, 101385, 2023 | 7 | 2023 |
| Reducing the number of mean-square deviation calculations with floating close structure in metadynamics J Pazúriková, A Křenek, V Spiwok, M Šimková The Journal of Chemical Physics 146 (11), 2017 | 4 | 2017 |
| Accelerated RMSD calculation for molecular metadynamics J Filipovič, J Pazúriková, A Křenek, V Spiwok 30th European Simulation and Modelling Conference, Reproduct NV, Ghent …, 2016 | 4 | 2016 |
| Property Map Collective Variable as a Useful Tool for a Force Field Correction D Trapl, M Krupicka, V Visnovsky, J Hozzová, J Ol’ha, A Krenek, V Spiwok Journal of Chemical Information and Modeling 62 (3), 567-576, 2022 | 3 | 2022 |
| Searching CUDA code autotuning spaces with hardware performance counters: data from benchmarks running on various GPU architectures J Hozzová, J Filipovič, A Nezarat, J Ol’ha, F Petrovič Data in Brief 39, 107631, 2021 | 3 | 2021 |
| Convergence of parareal algorithm applied on molecular dynamics simulations J Pazúriková, L Matyska Proceedings of MEMICS, 101-111, 2014 | 3 | 2014 |
| Estimating resource budgets to ensure autotuning efficiency J Olha, J Hozzová, M Antol, J Filipovič Parallel Computing, 103126, 2025 | 2 | 2025 |
| Improving ligand transport trajectory within flexible receptor in CaverDock P Němcová, J Hozzová, J Filipovič Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing, 619-626, 2022 | 2 | 2022 |
| Large-Scale Molecular Dynamics Simulations for Highly Parallel Infrastructures J Pazúriková arXiv preprint arXiv:1402.7216, 2014 | 2 | 2014 |
| Searching CUDA code autotuning spaces with hardware performance counters: data from benchmarks running on various GPU architectures J Filipovič, J Hozzová, A Nezarat, J Oľha, F Petrovič arXiv preprint arXiv:2102.05299, 2021 | 1 | 2021 |
| Simulation of Ligand Transport in Receptors Using CaverDock J Hozzová, O Vávra, D Bednář, J Filipovič Protein-Ligand Interactions and Drug Design, 105-124, 2021 | 1 | 2021 |
| Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations J Pazúriková, J Oľha, A Křenek, V Spiwok arXiv preprint arXiv:1801.02362, 2018 | 1 | 2018 |
| Accelerating Chemical Simulation through Model Modification J PAZÚRIKOVÁ Masarykova univerzita, Fakulta informatiky, 2018 | 1 | 2018 |
| FAIR Sharing of Data in Autotuning Research (Vision Paper) J Hozzová, JO Tørring, B van Werkhoven, D Strelák, R Vuduc Companion of the 15th ACM/SPEC International Conference on Performance …, 2024 | | 2024 |
