By Topic

Refinement of docked protein complex structures using evolutionary traces

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$33 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

4 Author(s)
Bahar Akbal-Delibas ; Department of Computer Science, University of Massachusetts Boston, Boston, MA, 02125 ; Irina Hashmi ; Amarda Shehu ; Nurit Haspel

Detection of protein complexes and their structures is crucial for understanding the role of protein complexes in the basic biology of organisms. Computational methods can provide researchers with a good starting point for the analysis of protein complexes. However, computational docking methods are often not accurate and their results need to be further refined to improve interface packing. In this paper, we introduce a novel refinement method that incorporates evolutionary information by employing an energy function containing Evolutionary Trace (ET)-based scoring function, which also takes shape complementarity, electrostatic and Van der Waals interactions into account. We tested our method on docked candidates of three protein complexes produced by a separate docking method. Our results suggest that the energy function can help biasing the results towards complexes with native interactions, filtering out false results. Our refinement method is able to produce structures with better RMSDs with respect to the known complexes and lower energies than those initial docked structures.

Published in:

Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on

Date of Conference:

12-15 Nov. 2011