Julie Bernauer et al 2005 Phys. Biol. 2 S17 doi:10.1088/1478-3975/2/2/S02
A docking analysis of the statistical physics of protein–protein recognition
Julie Bernauer1, Anne Poupon1, Jérôme Azé2 and Joël Janin3
Show affiliationsWe describe protein–protein recognition within the frame of the random energy model of statistical physics. We simulate, by docking the component proteins, the process of association of two proteins that form a complex. We obtain the energy spectrum of a set of protein–protein complexes of known three-dimensional structure by performing docking in random orientations and scoring the models thus generated. We use a coarse protein representation where each amino acid residue is replaced by its Voronoï cell, and derive a scoring function by applying the evolutionary learning program ROGER to a set of parameters measured on that representation. Taking the scores of the docking models to be interaction energies, we obtain energy spectra for the complexes and fit them to a Gaussian distribution, from which we derive physical parameters such as a glass transition temperature and a specificity transition temperature.
- PACS
- Subjects
- Dates
-
Issue 2 (June 2005)
Received 1 February 2005, accepted for publication 12 April 2005
Published 13 May 2005
-
-
A docking analysis of the statistical physics of protein–protein recognition
Julie Bernauer et al 2005 Phys. Biol. 2 S17
-
One compact analytic expression of the diatomic centrifugal distortion constants to any order
H Kobeissi and M Korek 1993 J. Phys. B: At. Mol. Opt. Phys. 26 L35
-
Annealed Treatment Effect in Poly(3-hexylthiophene):Methanofullerene Solar Cells
Yu Huang-Zhong and Peng Jun-Biao 2008 Chinese Phys. Lett. 25 1411
-
Beam dynamics of muon acceleration for neutrino factory
S A Bogacz 2003 J. Phys. G: Nucl. Part. Phys. 29 1723
-
Spacetime foam at a TeV
Luis A Anchordoqui 2007 J. Phys.: Conf. Ser. 60 191
-
The size dependence of the Einstein temperature of the tellurium nanoparticles
H Ikemoto et al 2009 J. Phys.: Conf. Ser. 190 012126
-
Progress in the generation of the UTC(CNM) in terms of a virtual clock
J M López-Romero and N Díaz-Muñoz 2008 Metrologia 45 S59
-
Intensity-modulated radiotherapy optimization with gEUD-guided dose–volume objectives
Qiuwen Wu et al 2003 Phys. Med. Biol. 48 279
-
Impact of hierarchical modular structure on ranking of individual nodes in directed networks
Naoki Masuda et al 2009 New J. Phys. 11 113002
-
Particle production azimuthal asymmetries in a clustering of color sources model
I Bautista et al 2010 J. Phys. G: Nucl. Part. Phys. 37 015103
Users also read
What's this?Related review articles
What's this?- Mechanisms governing the control of mRNA translation
- Classes of fast and specific search mechanisms for proteins on DNA
- Recombinant protein scaffolds for tissue engineering