Mgr. Martin Maňák, Ph.D.

University of West Bohemia in Pilsen
Research assistant at NTIS
Member of Centre of Computer Graphics and Visualisation

Research Interests

Computational geometry
Computer graphics
Voronoi diagrams
Visualization of molecular structures

Teaching

The following materials are shared via GAPPS. Use your Orion login.

Algorithms and Competitive Programming 1 - KIV/ASP1
The Beauty of Computer Graphics - KIV/KPG

Publications

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2024 (1)

Evaluation of Approximate Reflectional Symmetry. Manak, M.; Podgorelec, D.; and Kolingerova, I. In Proceedings of the 19th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications - IVAPP, pages 734-740, 2024. INSTICC, SciTePress
doi link bibtex

@inproceedings{Manak2024,
author={Manak, Martin and Podgorelec, David and Kolingerova, Ivana},
title={Evaluation of Approximate Reflectional Symmetry},
booktitle={Proceedings of the 19th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications - IVAPP},
year={2024},
pages={734-740},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0012472800003660},
isbn={978-989-758-679-8},
issn={2184-4321},
}

2022 (2)

Compact storage of additively weighted Voronoi diagrams. Manak, M.; Anikeenko, A.; Vasa, L.; and Kolingerova, I. The Visual Computer. 2022.

Compact storage of additively weighted Voronoi diagrams [link]

Paper doi link bibtex 1 download

@article{Manak2022,
author = {Manak, Martin and Anikeenko, Alexey and Vasa, Libor and Kolingerova, Ivana},
title = {Compact storage of additively weighted Voronoi diagrams},
journal = {The Visual Computer},
volume = {},
year = {2022},
pages = {},
issn = {1432-2315},
doi = {10.1007/s00371-022-02667-z},
url = {https://doi.org/10.1007/s00371-022-02667-z},
}

Rotational symmetry detection in 3D using reflectional symmetry candidates and quaternion-based rotation parameterization. Hruda, L.; Kolingerova, I.; Lavicka, M.; and Manak, M. Computer Aided Geometric Design, 98: 102138. 2022.

Rotational symmetry detection in 3D using reflectional symmetry candidates and quaternion-based rotation parameterization [link]

Paper doi link bibtex

@article{Hruda2022,
author = {Lukas Hruda and Ivana Kolingerova and Miroslav Lavicka and Martin Manak},
title = {Rotational symmetry detection in 3D using reflectional symmetry candidates and quaternion-based rotation parameterization},
journal = {Computer Aided Geometric Design},
volume = {98},
pages = {102138},
year = {2022},
issn = {0167-8396},
doi = {10.1016/j.cagd.2022.102138},
url = {https://www.sciencedirect.com/science/article/pii/S0167839622000747},
}

2020 (2)

Predictive compression of molecular dynamics trajectories. Dvorak, J.; Manak, M.; and Vasa, L. Journal of Molecular Graphics and Modelling, 96: 107531. 2020.

Predictive compression of molecular dynamics trajectories [link]

Paper doi link bibtex

@article{Dvorak2020,
author = {Jan Dvorak and Martin Manak and Libor Vasa},
title = {Predictive compression of molecular dynamics trajectories},
journal = {Journal of Molecular Graphics and Modelling},
volume = {96},
year = {2020},
pages = {107531},
issn = {1093-3263},
doi = {10.1016/j.jmgm.2020.107531},
url = {http://www.sciencedirect.com/science/article/pii/S1093326319306564},
}

Kinetic locally minimal triangulation: theoretical evaluation and combinatorial analysis. Vomacka, T.; Kolingerova, I.; and Manak, M. The Visual Computer, 36: 757-765. 2020.

Kinetic locally minimal triangulation: theoretical evaluation and combinatorial analysis [link]

Paper doi link bibtex

@article{Vomacka2019,
author = {Vomacka, Tomas and Kolingerova, Ivana and Manak, Martin},
title = {Kinetic locally minimal triangulation: theoretical evaluation and combinatorial analysis},
journal = {The Visual Computer},
volume = {36},
number = {},
pages = {757-765},
doi = {10.1007/s00371-019-01657-y},
url = {https://doi.org/10.1007/s00371-019-01657-y},
year = {2020},
}

2019 (2)

Exit regions of cavities in proteins. Manak, M.; Anikeenko, A.; and Kolingerova, I. In 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE), pages 1-6, 2019.
doi link bibtex

@inproceedings{Manak2019b,
author = {Manak, Martin and Anikeenko, Alexey and Kolingerova, Ivana},
title = {Exit regions of cavities in proteins},
booktitle = {2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)},
pages = {1-6},
doi = {10.1109/BIBE.2019.00010},
year = {2019},
}

Voronoi-based detection of pockets in proteins defined by large and small probes. Manak, M. Journal of Computational Chemistry, 40(19): 1758-1771. 2019.

Voronoi-based detection of pockets in proteins defined by large and small probes [link]

Paper doi link bibtex

@article{Manak2019a,
author = {Manak, Martin},
title = {Voronoi-based detection of pockets in proteins defined by large and small probes},
journal = {Journal of Computational Chemistry},
volume = {40},
number = {19},
pages = {1758-1771},
doi = {10.1002/jcc.25828},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.25828},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.25828},
year = {2019},
}

2018 (3)

Neighbourhood Graphs and Locally Minimal Triangulations. Kolingerova, I.; Vomacka, T.; Manak, M.; and Ferko, A. In Gavrilova, M. L.; and Tan, C. K., editor(s), Transactions on Computational Science XXXIII, pages 115-127, Berlin, Heidelberg, 2018. Springer Berlin Heidelberg

Neighbourhood Graphs and Locally Minimal Triangulations [link]

Paper doi link bibtex

@inproceedings{Kolingerova2018,
author = {Kolingerova, Ivana and Vomacka, Tomas and Manak, Martin and Ferko, Andrej},
editor = {Gavrilova, Marina L. and Tan, C.J. Kenneth},
title = {Neighbourhood Graphs and Locally Minimal Triangulations},
booktitle = {Transactions on Computational Science XXXIII},
year = {2018},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
pages = {115-127},
isbn={978-3-662-58039-4},
doi={10.1007/978-3-662-58039-4_7},
url={https://doi.org/10.1007/978-3-662-58039-4_7},
}

Computing the solvent excluded volume by GPU-based ray casting. Manak, M. In IADIS International Conference on Computer Graphics, Visualization, Computer Vision and Image Processing 2018 (part of MCCSIS 2018), pages 299-306, 2018.

Computing the solvent excluded volume by GPU-based ray casting [link]

Paper link bibtex 2 downloads

@inproceedings{Manak2018,
title = {Computing the solvent excluded volume by {GPU}-based ray casting},
author = {Martin Manak},
booktitle = {IADIS International Conference on Computer Graphics, Visualization, Computer Vision and Image Processing 2018 (part of MCCSIS 2018)},
year = {2018},
pages = {299-306},
isbn = {978-989-8533-79-1},
url={http://www.iadisportal.org/digital-library/computing-the-solvent-excluded-volume-by-gpu-based-ray-casting},
}

CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Jurcik, A.; Bednar, D.; Byska, J.; Marques, S. M; Furmanova, K.; Daniel, L.; Kokkonen, P.; Brezovsky, J.; Strnad, O.; Stourac, J.; Pavelka, A.; Manak, M.; Damborsky, J.; and Kozlikova, B. Bioinformatics, 34(20): 3586-3588. 2018.

CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories [link]

Paper doi link bibtex

@article{Jurcik2018,
author = {Jurcik, Adam and Bednar, David and Byska, Jan and Marques, Sergio M and Furmanova, Katarina and Daniel, Lukas and Kokkonen, Piia and Brezovsky, Jan and Strnad, Ondrej and Stourac, Jan and Pavelka, Antonin and Manak, Martin and Damborsky, Jiri and Kozlikova, Barbora},
title = {CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories},
journal = {Bioinformatics},
volume = {34},
number = {20},
pages = {3586-3588},
year = {2018},
doi = {10.1093/bioinformatics/bty386},
url = {https://doi.org/10.1093/bioinformatics/bty386},
}

2017 (3)

Hybrid Voronoi diagrams, their computation and reduction for applications in computational biochemistry. Manak, M.; Zemek, M.; Szkandera, J.; Kolingerova, I.; Papaleo, E.; and Lambrughi, M. Journal of Molecular Graphics and Modelling, 74: 225-233. 2017.

Hybrid Voronoi diagrams, their computation and reduction for applications in computational biochemistry [link]

Paper doi link bibtex

@article{Manak2017225,
author = {Martin Manak and Michal Zemek and Jakub Szkandera and Ivana Kolingerova and Elena Papaleo and Matteo Lambrughi},
title = {Hybrid {Voronoi} diagrams, their computation and reduction for applications in computational biochemistry},
journal = {Journal of Molecular Graphics and Modelling},
volume = {74},
number = {},
pages = {225-233},
year = {2017},
issn = {1093-3263},
doi = {10.1016/j.jmgm.2017.03.018},
url = {http://www.sciencedirect.com/science/article/pii/S1093326316304272},
}

Path Planning for Groups on Graphs. Szkandera, J.; Kolingerova, I.; and Manak, M. Procedia Computer Science, 108: 2338-2342. 2017. International Conference on Computational Science, ICCS 2017, 12-14 June 2017, Zurich, Switzerland

Path Planning for Groups on Graphs [link]

Paper doi link bibtex

@article{Szkandera2017,
author = {Szkandera, Jakub and Kolingerova, Ivana and Manak, Martin},
title = {Path Planning for Groups on Graphs},
journal = {Procedia Computer Science},
volume = {108},
pages = {2338-2342},
year = {2017},
note = {International Conference on Computational Science, ICCS 2017, 12-14 June 2017, Zurich, Switzerland},
issn = {1877-0509},
doi = {https://doi.org/10.1016/j.procs.2017.05.040},
url = {http://www.sciencedirect.com/science/article/pii/S1877050917305574},
}

Interactive Analysis of Connolly Surfaces for Various Probes. Manak, M.; Jirkovsky, L.; and Kolingerova, I. Computer Graphics Forum, 36(6): 160-172. sep 2017.

Interactive Analysis of Connolly Surfaces for Various Probes [link]

Paper doi link bibtex

@article{CGF:CGF12870,
author  = {Martin Manak and Lukas Jirkovsky and Ivana Kolingerova},
title   = {Interactive Analysis of {Connolly} Surfaces for Various Probes},
journal = {Computer Graphics Forum},
volume  = {36},
number  = {6},
issn    = {1467-8659},
url     = {http://dx.doi.org/10.1111/cgf.12870},
doi     = {10.1111/cgf.12870},
pages   = {160-172},
year    = {2017},
month   = {sep},
}

2016 (2)

Exploration of Empty Space among Spherical Obstacles via Additively Weighted Voronoi Diagram. Manak, M. Computer Graphics Forum, 35(5): 249-258. 2016. Symposium on Geometry Processing 2016

Exploration of Empty Space among Spherical Obstacles via Additively Weighted Voronoi Diagram [link]

Paper doi link bibtex

@article{10.1111:cgf.12980,
author  = {Martin Manak},
title   = {Exploration of Empty Space among Spherical Obstacles via Additively Weighted {Voronoi} Diagram},
journal = {Computer Graphics Forum},
volume  = {35},
number  = {5},
pages   = {249-258},
year    = {2016},
url     = {http://diglib.eg.org/handle/10.1111/cgf12980},
doi     = {10.1111/cgf.12980},
issn    = {1467-8659},
publisher = {The Eurographics Association and John Wiley & Sons Ltd.},
note    = {Symposium on Geometry Processing 2016},
}

Extension of the edge tracing algorithm to disconnected Voronoi skeletons. Manak, M.; and Kolingerova, I. Information Processing Letters, 116(2): 85-92. feb 2016.

Extension of the edge tracing algorithm to disconnected Voronoi skeletons [link]

Paper doi link bibtex

@article{Manak2016,
author  = {Martin Manak and Ivana Kolingerova},
title   = {Extension of the edge tracing algorithm to disconnected {Voronoi} skeletons},
journal = {Information Processing Letters},
volume  = {116},
number  = {2},
pages   = {85-92},
year    = {2016},
doi     = {10.1016/j.ipl.2015.09.017},
url     = {http://www.sciencedirect.com/science/article/pii/S002001901500174X},
issn    = {0020-0190},
month   = {feb},
}

2014 (1)

CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. Kozlikova, B.; Sebestova, E.; Sustr, V.; Brezovsky, J.; Strnad, O.; Daniel, L.; Bednar, D.; Pavelka, A.; Manak, M.; Bezdeka, M.; Benes, P.; Kotry, M.; Gora, A. W.; Damborsky, J.; and Sochor, J. Bioinformatics, 30(18): 2684-2685. 2014.
doi link bibtex

@article{CaverAnalyst2014,
author  = {Barbora Kozlikova and Eva Sebestova and Vilem Sustr and Jan Brezovsky and Ondrej Strnad and Lukas Daniel and David Bednar and Antonin Pavelka and Martin Manak and Martin Bezdeka and Petr Benes and Matus Kotry and Artur Wiktor Gora and Jiri Damborsky and Jiri Sochor},
title   = {{CAVER Analyst} 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures},
journal = {Bioinformatics},
year    = {2014},
volume  = {30},
number  = {18},
pages   = {2684-2685},
doi     = {10.1093/bioinformatics/btu364},
}

2011 (1)

Advanced Space Filtering for the Construction of 3D Additively Weighted Voronoi Diagram. Zemek, M.; Manak, M.; and Kolingerova, I. In The Fifth International Conference on Advanced Engineering Computing and Applications in Sciences, of ADVCOMP, pages 37-43, 2011. IARIA
link bibtex

@inproceedings{ZemekManakKolingerova2011,
author    = {Michal Zemek and Martin Manak and Ivana Kolingerova},
title     = {Advanced Space Filtering for the Construction of {3D} Additively Weighted {Voronoi} Diagram},
booktitle = {The Fifth International Conference on Advanced Engineering Computing and Applications in Sciences},
series    = {ADVCOMP},
year      = {2011},
pages     = {37-43},
publisher = {IARIA},
isbn      = {978-1-61208-172-4},
issn      = {2308-4499},
}

2010 (1)

Fast Discovery of Voronoi Vertices in the Construction of Voronoi Diagram of 3D Balls. Manak, M.; and Kolingerova, I. In Seventh International Symposium on Voronoi Diagrams in Science and Engineering, of ISVD, pages 95-104, 2010. IEEE Computer Society
doi link bibtex

@inproceedings{ManakKolingerova2010,
author    = {Martin Manak and Ivana Kolingerova},
title     = {Fast Discovery of {Voronoi} Vertices in the Construction of {Voronoi} Diagram of {3D} Balls},
booktitle = {Seventh International Symposium on Voronoi Diagrams in Science and Engineering},
series    = {ISVD},
year      = {2010},
pages     = {95-104},
publisher = {IEEE Computer Society},
isbn      = {978-0-7695-4112-9},
doi       = {10.1109/ISVD.2010.22},
}

2009 (1)

Inverted Ball as a Boundary-constraint for Voronoi Diagrams of 3D Spheres. Manak, M.; and Kolingerova, I. In 25th European Workshop on Computational Geometry, of EuroCG, pages 289-292, 2009.

Inverted Ball as a Boundary-constraint for Voronoi Diagrams of 3D Spheres [link]

Paper link bibtex

@inproceedings{ManakKolingerova2009,
author    = {Martin Manak and Ivana Kolingerova},
title     = {Inverted Ball as a Boundary-constraint for {Voronoi} Diagrams of {3D} Spheres},
booktitle = {25th European Workshop on Computational Geometry},
series    = {EuroCG},
year      = {2009},
pages     = {289-292},
url       = {http://2009.eurocg.org},
}

Illustrations

The following screenshots were rendered by CAVER Analyst, using our own plugin for the computation and visualization of molecular surfaces and cavities. Their computation is based on the additively weighted Voronoi diagram of atoms. Rendering uses GPU raycasting and geometry instancing.