Dr Konstantin Roeder | Wales Group

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My research focusses on multifunnel energy landscapes associated with most proteins, as wells as RNA and DNA strands.

As these landscapes can be easily perturbed in nature by mutations, we atttempt to understand these changes by computationally exploring the energy landscapes of various mutants for a given system. We then link changes in the energy landscape to shifts in the observed conformational ensembles, changed mechanistic pathways between ensembles, and other observable properties such as NMR shifts.

Publications

Improving double-ended transition state searches for soft-matter systems

K Röder, DJ Wales

– Journal of Chemical Physics

(2020)

153,

034104

(DOI: 10.1063/5.0011829)

Energy Landscapes of Deoxyxylo- A nd Xylo-Nucleic Acid Octamers

DJ Sharpe, K Röder, DJ Wales

– J Phys Chem B

(2020)

124,

4062

(DOI: 10.1021/acs.jpcb.0c01420)

Affinity-Selected Bicyclic Peptide G‑Quadruplex Ligands Mimic a Protein-like Binding Mechanism

KC Liu, K Röder, C Mayer, S Adhikari, DJ Wales, S Balasubramanian

– Journal of the American Chemical Society

(2020)

142,

8367

(DOI: 10.1021/jacs.0c01879)

Structural transitions in the RNA 7SK 5 ' hairpin and their effect on HEXIM binding

K Röder, G Stirnemann, A-C Dock-Bregeon, DJ Wales, S Pasquali

– Nucleic acids research

(2019)

48,

373

(DOI: 10.1093/nar/gkz1071)

Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems

K Röder, JA Joseph, BE Husic, DJ Wales

– Advanced Theory and Simulations

(2019)

2,

1800175

(DOI: 10.1002/adts.201800175)

Evolved Minimal Frustration in Multifunctional Biomolecules.

K Röder, DJ Wales

– The journal of physical chemistry. B

(2018)

122,

10989

(DOI: 10.1021/acs.jpcb.8b03632)

Mutational Basin-Hopping – Combined Structure and Sequence Optimisation for Biomolecules

K Röder, DJ Wales

– The journal of physical chemistry letters

(2018)

9,

6169

(DOI: 10.1021/acs.jpclett.8b02839)

Analysis of the Ub to Ub-CR transition in ubiquitin

K Röder, DJ Wales

– Biochemistry

(2018)

57,

6180

(DOI: 10.1021/acs.biochem.8b00770)

Predicting Pathways between Distant Configurations for Biomolecules

K Röder, DJ Wales

– Journal of Chemical Theory and Computation

(2018)

14,

4271

(DOI: 10.1021/acs.jctc.8b00370)

Predicting Pathways between Distant Configurations for Biomolecules

K Roder, DJ Wales

– JOURNAL OF CHEMICAL THEORY AND COMPUTATION

(2018)

14,

4271

(DOI: 10.1021/acs.jctc.8b00370)