TITLE

Designing coarse grained-and atom basedpotentials for protein-protein docking

AUTHOR(S)
Tobi, Dror
PUB. DATE
January 2010
SOURCE
BMC Structural Biology;2010, Vol. 10, p40
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s) upon binding. The major challenge is to define a scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations. Results: Using a linear programming (LP) technique, we developed two types of potentials: (i) Side chain-based and (ii) Heavy atom-based. To achieve this we considered a set of 161 transient complexes and generated a large set of putative docked structures (decoys), based on a shape complementarity criterion, for each complex. The demand on the potentials was to yield, for the native (correctly docked) structure, a potential energy lower than those of any of the non-native (misdocked) structures. We show that the heavy atom-based potentials were able to comply with this requirement but not the side chain-based one. Thus, despite the smaller number of parameters, the capability of heavy atom-based potentials to discriminate between native and "misdocked" conformations is improved relative to those of the side chain-based potentials. The performance of the atombased potentials was evaluated by a jackknife test on a set of 50 complexes taken from the Zdock2.3 decoys set. Conclusions: Our results show that, using the LP approach, we were able to train our potentials using a dataset of transient complexes only the newly developed potentials outperform three other known potentials in this test.
ACCESSION #
57229303

 

Related Articles

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics