Dominik Budday



Organisation


Chair of Applied Dynamics


Project member


Protein flexibility and conformational ensembles from kino-geometric modeling, sampling and motion planning.
Prof. Dr.-Ing. Sigrid Leyendecker
(01/06/2014)


Publications (Download BibTeX)

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Budday, D. (2019). High-Dimensional Robotics at the Nanoscale — Kino-Geometric Modeling of Proteins and Molecular Mechanisms (Dissertation).
Budday, D., Leyendecker, S., & van den Bedem, H. (2018). Bridging protein rigidity theory and normal modes using kino-geometric analysis. In Proceedings of the GAMM Annual Meeting. München, DE.
Fonseca, R., Budday, D., & van den Bedem, H. (2018). Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces. Journal of Computational Chemistry. https://dx.doi.org/10.1002/jcc.25138
Budday, D., Leyendecker, S., & van den Bedem, H. (2018). Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion. Journal of Chemical Information and Modeling, 58(10), 2108-2122. https://dx.doi.org/10.1021/acs.jcim.8b00267
Héliou, A., Budday, D., Fonseca, R., & van den Bedem, H. (2017). Fast, clash-free RNA conformational morphing using molecular junctions. Bioinformatics. https://dx.doi.org/10.1093/bioinformatics/btx127
Budday, D., Fonseca, R., Leyendecker, S., & van den Bedem, H. (2017). Frustration-guided motion planning reveals conformational transitions in proteins. Proteins-Structure Function and Bioinformatics, 85(10), 1795-1807. https://dx.doi.org/10.1002/prot.25333
Budday, D., Fonseca, R., Leyendecker, S., & van den Bedem, H. (2016). Clash- and constraint guided motion planning reveals conformational transition pathways in proteins. Poster presentation, Santa Monica, California, US.
Budday, D., Fonseca, R., Leyendecker, S., & van den Bedem, H. (2016). Frustration-guided motion planning reveals conformational transitions in proteins. Durham, North Carolina, US.
Budday, D., Fonseca, R., Leyendecker, S., & van den Bedem, H. (2016). Frustration-guided motion planning reveals conformational transitions in proteins. In Proceedings of the 3DSIG. Orlando, Florida, US.
Budday, D., Fonseca, R., Héliou, A., Leyendecker, S., & van den Bedem, H. (2016). Navigating protein conformation spaces by kino-geometric sampling and modulating frustrated motions. Poster presentation at Annual Meeting of the German Biophysical Society, Erlangen, DE.

Last updated on 2016-05-05 at 05:17