SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies. - Andrey Alekseenko; Olga Kononova; Yaroslav Kholodov; Kenneth A. Marx; Valeri Barsegov (J. Comput. Chem., 2016)

Bayesian Localization for Autonomous Vehicle using Sensor Fusion and Traffic Signs. - Sergey Verentsov; Emil Magerramov; Vlad Vinogradov; Ramil Gizatullin; Andrey Alekseenko; Yaroslav Kholodov; Evgeniy Nikolskiy (ICRAI, 2017)

Adaptive traffic light control on highway entrances. - Andrey Alekseenko; Yaroslav Kholodov; Aleksander Kholodov; Yuri V. Chekhovich; Vsevolod Starozhilets (ITSC, 2017)

Bayesian Framework for Vehicle Localization Using Crowdsourced Data. - Sergey Verentsov; Emil Magerramov; Vlad Vinogradov; Ramil Gizatullin; Andrey Alekseenko; Yaroslav Kholodov; Evgeniy Nikolskiy (Intelligent Vehicles Symposium, 2018)

Protein-ligand docking using FFT based sampling: D3R case study. - Dzmitry Padhorny; David R. Hall; Hanieh Mirzaei; Artem B. Mamonov; Mohammad Moghadasi; Andrey Alekseenko; Dmitri Beglov; Dima Kozakov (J. Comput. Aided Mol. Des., 2018)

ITS+DM Hackathon (ITSC 2017): Lane Departure Prediction With Naturalistic Driving Data. - Andrey Alekseenko; Hien Q. Dang; Gaurav Bansal; Javier J. Sánchez Medina; Chiyomi Miyajima; Takatsugu Hirayama; Kazuya Takeda; Ichiro Ide (IEEE Intell. Transp. Syst. Mag., 2019)

Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. - Mikhail Ignatov; Cong Liu 031; Andrey Alekseenko; Zhuyezi Sun; Dzmitry Padhorny; Sergei Kotelnikov; Andrey M. Kazennov; Ivan Grebenkin; Yaroslav Kholodov; Istvan Kolosvari; Alberto Pérez; Ken A. Dill; et al. (J. Comput. Aided Mol. Des., 2019)

Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. - Sergei Kotelnikov; Andrey Alekseenko; Cong Liu 031; Mikhail Ignatov; Dzmitry Padhorny; Emiliano Brini; Mark Lukin; Evangelos A. Coutsias; Ken A. Dill; Dima Kozakov (J. Comput. Aided Mol. Des., 2020)

Experiences With Adding SYCL Support to GROMACS. - Andrey Alekseenko; Szilárd Páll; Erik Lindahl (IWOCL, 2021)

Comparing the Performance of SYCL Runtimes for Molecular Dynamics Applications. - Andrey Alekseenko; Szilárd Páll (IWOCL, 2023)

GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability. - Andrey Alekseenko; Szilárd Páll; Erik Lindahl (CoRR, 2024)