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Prediction of Protein-Protein Binding Interfaces

Chapter
Part of the Focus on Structural Biology book series (FOSB, volume 8)

Abstract

When it comes to regulating protein activity, complexation mechanisms are just as important as ligand binding. Most proteins never exist in isolation – instead they serve as building blocks for more complex systems. Some proteins form multimers to ensure maintain spatial alignment (required e.g. for phase separation in the dual lipid layer and formation of hydrophilic compartments in ion channels (Unwin 2005; Jasti et al.. 2007)); others may require temporary binding of cofactors (e.g. regulation of transcription factors (Huxford et al. 1998)), or are part of complicated protein machinery (e.g. proton-driven rotors in ATP synthases (Boyer 1997; Oster and Wang 1999, 2003)).

Keywords

HADDOCK ZDOCK RosettaDock Oil drop Sequence conservation Mutagenesis Epitope mapping H-D exchange Crosslinking experiments Solvated docking Ambiguous Interaction Restraints (AIRs) Rotamer packing Side-chain rotamer probabilities Monte Carlo-based modeling package Geometric alignment Fast Fourier Transform algorithms CHARMM forcefields Homodimer Pair-wise interaction Lock-key Fuzzy oil drop 

Notes

Acknowledgements

The presented research was carried out in 1995–2011 and funded by a series of grants from the Jagiellonian University Medical College. The Academic Computing Center CYFRONET AGH Krakow provided computational support. We would like to express our gratitude to Piotr Nowakowski of CYFRONET AGH for valuable editorial remarks. Technical support provided by Anna Zaremba-Śmietańska is also gratefully acknowledged.

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Department of Bioinformatics and TelemedicineJagiellonian University – Medical CollegeCracowPoland
  2. 2.Faculty of Physics, Astronomy and Applied Computer ScienceJagiellonian UniversityCracowPoland
  3. 3.Computational Biology Group, Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch-BelvalLuxembourg

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