Budday, Dominik

Dr.-Ing.

Dominik Budday, Dr.-Ing.

Immerwahrstrasse 1
91058 Erlangen
Germany

    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

 

reviewed journal publications

2020

2018

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2015

 

conferences and proceedings

2019

2018

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2014

2012

 

further publications

 

  • Protein flexibility and conformational ensembles from kino-geometric modeling and sampling to motion planning

    (Own Funds)

    Term: 2014-06-01 - 2019-03-31

    Proteins 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.