Dominik Budday
Dominik Budday, Dr.-Ing.
- 2011 B.Sc., Bachelor in Mechanical Engineering, Karlsruhe Institute of Technology
- 2014 M.Sc., Master in Mechanical Engineering, Karlsruhe Institute of Technology
- 2014 -2018 Doctoral candidate, Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg
- 2018 Dr.-Ing., PhD in Engineering, Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg
- 2019 postdoc, Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg
theses
2019
- Budday D.:
High-Dimensional Robotics at the Nanoscale — Kino-Geometric Modeling of Proteins and Molecular Mechanisms (Dissertation, 2019)
2014
- Budday D.:
Driver behavior classification and warning strategies for stop controlled intersection approaches (Master thesis, 2014)
2011
- Budday D.:
Aufbau und Analyse eines passiven Modells für das räumliche Gehen (Bachelor thesis, 2011)
reviewed journal publications
2020
- Kergaßner A., Burkhardt C., Lippold D., Kergaßner M., Pflug L., Budday D., Steinmann P., Budday S.:
Memory-based meso-scale modeling of Covid-19
In: Computational Mechanics (2020)
ISSN: 0178-7675
DOI: 10.1007/s00466-020-01883-5
2018
- Budday D., Leyendecker S., van den Bedem H.:
Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion
In: Journal of Chemical Information and Modeling 58 (2018), p. 2108-2122
ISSN: 1549-9596
DOI: 10.1021/acs.jcim.8b00267
URL: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.8b00267?journalCode=jcisd8 - Fonseca R., Budday D., van den Bedem H.:
Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces
In: Journal of Computational Chemistry (2018)
ISSN: 0192-8651
DOI: 10.1002/jcc.25138
2017
- Budday D., Fonseca R., Leyendecker S., van den Bedem H.:
Frustration-guided motion planning reveals conformational transitions in proteins
In: Proteins-Structure Function and Bioinformatics 85 (2017), p. 1795-1807
ISSN: 0887-3585
DOI: 10.1002/prot.25333 - Héliou A., Budday D., Fonseca R., van den Bedem H.:
Fast, clash-free RNA conformational morphing using molecular junctions
In: Bioinformatics (2017)
ISSN: 1367-4803
DOI: 10.1093/bioinformatics/btx127
2015
- Budday D., Leyendecker S., van den Bedem H.:
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations
In: Journal of the Mechanics and Physics of Solids 83 (2015), p. 36-47
ISSN: 0022-5096
DOI: 10.1016/j.jmps.2015.06.006
conferences and proceedings
2019
- Budday D., Leyendecker S., van den Bedem H.:
Kino‐Geometric Modeling: Insights into Protein Molecular Mechanisms
GAMM Annual Meeting (Vienna, 2019-02-18 - 2019-02-22)
In: Proc. Appl. Math. Mech (PAMM) 2019
DOI: 10.1002/pamm.201900448
2018
- Budday D., Fonseca R., Héliou A., Leyendecker S., van den Bedem H.:
Functional insights from kino-geometric modeling of macromolecules
9 Workshop junger Nachwuchwissenschafler in der Mechanik (Zell am See, Austria, 2018-02-18 - 2018-02-22) - Budday D., Leyendecker S., van den Bedem H.:
Bridging protein rigidity theory and normal modes using kino-geometric analysis
GAMM Annual Meeting (Munich, 2018-03-19 - 2018-03-23)
In: Proc. Appl. Math. Mech. (PAMM) 2018
DOI: 10.1002/pamm.201800251 - Budday D., Leyendecker S., van den Bedem H.:
Bridging protein rigidity theory and normal modes using kino-geometric analysis with hierarchical constraint relaxation
GAMM Annual Meeting (Munich, 2018-03-19 - 2018-03-23)
In: Proc. Appl. Math. Mech. (PAMM) 2018
DOI: 10.1002/pamm.201800251
2017
- Budday D., Fonseca R., Héliou A., Leyendecker S., van den Bedem H.:
Revealing molecular mechanisms with kino-geometric modeling macromolecules
Presentation, Kortemme Lab at UCSF (San Francisco, California)
2016
- Budday D., Fonseca R., Héliou A., Leyendecker S., van den Bedem H.:
Navigating protein conformation spaces by kino-geometric sampling and modulating frustrated motions
Annual Meeting of the German Biophysical Society (Erlangen, 2016-09-25 - 2016-09-28) - Budday D., Fonseca R., Leyendecker S., van den Bedem H.:
Clash- and constraint guided motion planning reveals conformational transition pathways in proteins
Poster (Santa Monica, California) - Budday D., Fonseca R., Leyendecker S., van den Bedem H.:
Frustration-guided motion planning reveals conformational transitions in proteins
3DSIG (Orlando, Florida, 2016-04-17 - 2016-04-21) - Budday D., Fonseca R., Leyendecker S., van den Bedem H.:
Frustration-guided motion planning reveals conformational transitions in proteins
Conference presentation (Durham, North Carolina)
2015
- Budday D., Leyendecker S., van den Bedem H.:
A geometric approach to characterize rigidity in proteins
GAMM Annual Meeting (Lecce, 2015-03-23 - 2015-03-27)
In: Proc. Appl. Math. Mech (PAMM) 2015
DOI: 10.1002/pamm.201510035 - Budday D., Leyendecker S., van den Bedem H.:
A geometric approach to characterize rigidity of biomolecules
EMI Conference, Stanford University (California, 2015-06-16 - 2015-06-19) - Budday D., Leyendecker S., van den Bedem H.:
Protein conformational analysis using kino-geometric constraints
2014
- Budday D., Leyendecker S., van den Bedem H.:
Characterizing rigidity in biomolecules with geometric tools
BaMBA 9 (California, 2014-11-22 - 2014-11-22)
2012
- Bauer F., Seipel J., Budday D.:
Stability and robustness of a 3D SLIP model for walking using lateral leg placement control
ASME (Chicago, 2012-08-12 - 2012-08-12)
In: Proceedings of the ASME 2012
DOI: 10.1115/DETC2012-71154
further publications
-
Protein flexibility and conformational ensembles from kino-geometric modeling and sampling to motion planning
(Own Funds)
Term: 2014-06-01 - 2019-03-31Proteins are dynamic macromolecules that perform their biological functions by exchanging between different conformational substates on a broad range of spatial and temporal scales. As the underlying energy landscapes that govern these conformational changes are very rough and often contain high energy barriers, efficient, yet atomically detailed simulations to understand and predict biophysically relevant motions remain challenging.
This project aims at providing functional insights into protein molecular mechanisms from simplified kinematic and geometric modeling. Guided by the covalent bond structure of the molecule, we construct kinematic multi-body systems with dihedral degrees of freedom and non-covalent interactions as constraints, which allows us to efficiently analyze conformational flexibility and deform the protein while maintaining secondary structure. Our analyses show convincing agreement with experimental data from various resources and more detailed Molecular Dynamics simulations, demonstrating the power of kino-geometric models for fast insights into protein flexibility and functional mechanisms, with broad implications for drug design and human health.