Volume 6 Supplement 1

9th German Conference on Chemoinformatics

Open Access

Elucidating protein-protein interactions using the HYDE scoring function

  • Eva Vennmann1,
  • Nadine Schneider1,
  • Gudrun Lange2 and
  • Matthias Rarey1
Journal of Cheminformatics20146(Suppl 1):P36

https://doi.org/10.1186/1758-2946-6-S1-P36

Published: 11 March 2014

Protein-protein interactions take place in every aspect of life. The diversity of those interactions and their significant role in regulatory pathways account for the special interest in them. As shown in various diseases, protein-protein interactions can be deregulated and the cause of illness. Therefore, a better and more detailed understanding of protein-protein interactions is of great importance.

Protein-protein interactions can be classified according to their stability into permanent, long-lasting or transient, functionality-dependent complexes [1]. The latter ones are of special interest for using them to influence regulatory pathways. Deeper insights into protein-protein interactions can be achieved by comprehending the stability of protein-protein complexes and especially of the interface in all its details.

In our study we analyzed the stability of protein-protein interactions using the recently developed HYDE scoring function [24]. HYDE consistently describes hydrogen bonds, the hydrophobic effect and polar dehydration and has been proved successful in estimating protein-ligand binding affinities. In this way, HYDE enables to estimate the stability of protein-protein interactions as well as the energetical contribution of single amino acids e.g. to identify so called ‘hotspot’ residues.

Authors’ Affiliations

(1)
Center for Bioinformatics, University of Hamburg
(2)
Bayer CropScience AG, Industriepark Hoechst, G836

References

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Copyright

© Vennmann et al; licensee Chemistry Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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