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PEDS Advance Access published online on March 8, 2004
Protein Engineering Design and Selection, doi:10.1093/protein/gzh021
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Received November 26, 2003
Revised January 26, 2004
Accepted January 26, 2004
Oxford University Press

Article

A novel method for scoring of docked protein complexes using predicted protein-protein binding sites

Kay-Eberhard Gottschalk 1, Hani Neuvirth 1, and Gideon Schreiber 1*

1 Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100 Israel

* To whom correspondence should be addressed. E-mail: gideon.schreiber{at}weizmann.ac.il.


  Abstract

Docking algorithms produce many possible structures of a protein-protein complex. In most cases some of them resemble the correct structure within a RMSD of less than 3 Å. A major challenge in the field of docking is to extract the correct structure out of this pool, the so called ‘scoring’. Here, we introduce a new scoring function, which discriminates between the many wrong and few true conformations. The scoring function is based on measuring the tightness of fit of the two docked proteins at a predicted binding interface. The location of the binding interface is identified using ProMate, a computer algorithm recently developed by us. The new scoring function does not rely on energy considerations. It is therefore tolerant to low-resolution descriptions of the interface. A linear relation between the score and the RMSD relative to the ‘true structure’ is found in most of the cases evaluated. The function was tested on the docking results of 21 complexes in their unbound form. It was found to be successful in 77% of the examined cases, defining success as scoring a ‘true’ result with a P value of better than 0.1.

Keywords: Docking, protein-protein interaction, scoring function, interface-prediction


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