On the binding affinity of macromolecular interactions: daring to ask why proteins interact by Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin Interface Volume 10(79): February 6, 2013 ©2013 by The Royal Society

Methodology to follow in protein–protein interaction identification leading to drug/interface design. Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

Change in the number of intermolecular interactions for 195 protein–protein complexes using cut-offs ±1 Å. μ corresponds to the average value calculated. Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

(a,b) Crystallographically determined structures of ubiquitin (PDB entries 1UBQ and 1UBI), along with their corresponding crystallographic water molecules. Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

Simulated scatchard plot for Ran GTPase-GDP and importin β. Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

(a,b) Isothermal titration calorimetry and (c,d) surface plasmon resonance (SPR) techniques. Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

The three basic mechanisms proposed for molecular recognition: (a) lock and key, (b) induced fit, and (c) conformational selection (dynamic fit). Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

Conformational changes in protein–protein complexes; unbound conformations are shown in greyscale, whereas bound conformations are shown in colour code by assigning a secondary structure; (a) the complex between thioredoxin reductase and thioredoxin is illu... Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

Water in protein–protein interactions and the explanation of the Chothia–Janin theory for the affinity of protein–protein complexes; (a) intermolecular interactions are recovered in the bound conformation, being already present with the molecules of the sol... Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

Schematic of the energy landscape of two different protein–protein complexes. Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society

Correlations between some energetic components of the HADDOCK score [217] ((a) van der Waals interactions; (b) desolvation energy) and experimental koff for 54 protein–protein complexes [98,133]. Panagiotis L. Kastritis, and Alexandre M. J. J. Bonvin J. R. Soc. Interface 2013;10: ©2013 by The Royal Society