elucidating protein-protein interactions using the hyde scoring function

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POSTER PRESENTATION Open Access Elucidating protein-protein interactions using the HYDE scoring function Eva Vennmann 1* , Nadine Schneider 1 , Gudrun Lange 2 , Matthias Rarey 1 From 9th German Conference on Chemoinformatics Fulda, Germany. 10-12 November 2013 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 interac- tions 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 [2-4]. 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 iden- tify so called hotspotresidues. Authorsdetails 1 Center for Bioinformatics, University of Hamburg, Bundestr.43, 20146 Hamburg, Germany. 2 Bayer CropScience AG, Industriepark Hoechst, G836, 65926 Frankfurt am Main, Germany. Published: 11 March 2014 References 1. Nooren I, Thornton J: Diversity of protein-protein interactions. EMBO J 2003, 22(14):3486-3492. 2. Reulecke I, Lange G, Albrecht J, Klein R, Rarey M: Towards an Integrated Description of Hydrogen Bonding and Dehydration: Decreasing False Positives in Virtual Screening with the HYDE Scoring Function. ChemMedChem 2008, 3(6):885-897. 3. Schneider N, Klein R, Lange G, Rarey M: Nearly no Scoring Function without a Hansch-Analysis. Molecular Informatics 2012, 31(6-7):503-507. 4. Schneider N, Lange G, Hindle S, Klein R, Rarey M: A consistent description of HYdrogen bond and DEhydration energies in proteinligand complexes: methods behind the HYDE scoring function. Journal of Computer- Aided Molecular Design 2013, 27(1):15-29. doi:10.1186/1758-2946-6-S1-P36 Cite this article as: Vennmann et al.: Elucidating protein-protein interactions using the HYDE scoring function. Journal of Cheminformatics 2014 6(Suppl 1):P36. Open access provides opportunities to our colleagues in other parts of the globe, by allowing anyone to view the content free of charge. Publish with ChemistryCentral and every scientist can read your work free of charge W. Jeffery Hurst, The Hershey Company. available free of charge to the entire scientific community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours you keep the copyright Submit your manuscript here: http://www.chemistrycentral.com/manuscript/ 1 Center for Bioinformatics, University of Hamburg, Bundestr.43, 20146 Hamburg, Germany Full list of author information is available at the end of the article Vennmann et al. Journal of Cheminformatics 2014, 6(Suppl 1):P36 http://www.jcheminf.com/content/6/S1/P36 © 2014 Vennmann et al; licensee Chemistry 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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Page 1: Elucidating protein-protein interactions using the HYDE scoring function

POSTER PRESENTATION Open Access

Elucidating protein-protein interactions using theHYDE scoring functionEva Vennmann1*, Nadine Schneider1, Gudrun Lange2, Matthias Rarey1

From 9th German Conference on ChemoinformaticsFulda, Germany. 10-12 November 2013

Protein-protein interactions take place in every aspect oflife. The diversity of those interactions and their significantrole in regulatory pathways account for the special interestin them. As shown in various diseases, protein-proteininteractions can be deregulated and the cause of illness.Therefore, a better and more detailed understanding ofprotein-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 areof special interest for using them to influence regulatorypathways. Deeper insights into protein-protein interac-tions can be achieved by comprehending the stability ofprotein-protein complexes and especially of the interfacein all its details.In our study we analyzed the stability of protein-protein

interactions using the recently developed HYDE scoringfunction [2-4]. HYDE consistently describes hydrogenbonds, the hydrophobic effect and polar dehydration andhas been proved successful in estimating protein-ligandbinding affinities. In this way, HYDE enables to estimatethe stability of protein-protein interactions as well as theenergetical contribution of single amino acids e.g. to iden-tify so called ‘hotspot’ residues.

Authors’ details1Center for Bioinformatics, University of Hamburg, Bundestr.43, 20146Hamburg, Germany. 2Bayer CropScience AG, Industriepark Hoechst, G836,65926 Frankfurt am Main, Germany.

Published: 11 March 2014

References1. Nooren I, Thornton J: Diversity of protein-protein interactions. EMBO J

2003, 22(14):3486-3492.

2. Reulecke I, Lange G, Albrecht J, Klein R, Rarey M: Towards an IntegratedDescription of Hydrogen Bonding and Dehydration: Decreasing FalsePositives in Virtual Screening with the HYDE Scoring Function.ChemMedChem 2008, 3(6):885-897.

3. Schneider N, Klein R, Lange G, Rarey M: Nearly no Scoring Functionwithout a Hansch-Analysis. Molecular Informatics 2012, 31(6-7):503-507.

4. Schneider N, Lange G, Hindle S, Klein R, Rarey M: A consistent descriptionof HYdrogen bond and DEhydration energies in protein–ligandcomplexes: methods behind the HYDE scoring function. Journal ofComputer- Aided Molecular Design 2013, 27(1):15-29.

doi:10.1186/1758-2946-6-S1-P36Cite this article as: Vennmann et al.: Elucidating protein-proteininteractions using the HYDE scoring function. Journal of Cheminformatics2014 6(Suppl 1):P36.

Open access provides opportunities to our colleagues in other parts of the globe, by allowing

anyone to view the content free of charge.

Publish with ChemistryCentral and everyscientist can read your work free of charge

W. Jeffery Hurst, The Hershey Company.

available free of charge to the entire scientific communitypeer reviewed and published immediately upon acceptancecited in PubMed and archived on PubMed Centralyours you keep the copyright

Submit your manuscript here:http://www.chemistrycentral.com/manuscript/

1Center for Bioinformatics, University of Hamburg, Bundestr.43, 20146Hamburg, GermanyFull list of author information is available at the end of the article

Vennmann et al. Journal of Cheminformatics 2014, 6(Suppl 1):P36http://www.jcheminf.com/content/6/S1/P36

© 2014 Vennmann et al; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction 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.