DocumentCode :
3523177
Title :
A new distributed algorithm for side-chain positioning in the process of protein docking
Author :
Moghadasi, Mohammad ; Kozakov, Dima ; Vakili, Pirooz ; Vajda, Szilard ; Paschalidis, Ioannis C.
Author_Institution :
Div. of Syst. Eng., Boston Univ., Boston, MA, USA
fYear :
2013
fDate :
10-13 Dec. 2013
Firstpage :
739
Lastpage :
744
Abstract :
Side-chain positioning (SCP) is an important component of computational protein docking methods. Existing SCP methods and available software have been designed for protein folding applications where side-chain positioning is also important. As a result they do not take into account significant special structure that SCP for docking exhibits. We propose a new algorithm which poses SCP as a Maximum Weighted Independent Set (MWIS) problem on an appropriately constructed graph. We develop an approximate algorithm which solves a relaxation of the MWIS and then rounds the solution to obtain a high-quality feasible solution to the problem. The algorithm is fully distributed and can be executed on a large network of processing nodes requiring only local information and message-passing between neighboring nodes. Motivated by the special structure in docking, we establish optimality guarantees for a certain class of graphs. Our results on a benchmark set of enzyme-inhibitor protein complexes show that our predictions are close to the native structure and are comparable to the ones obtained by a state-of-the-art method. The results are substantially improved if rotamers from unbound protein structures are included in the search. We also establish that the use of our SCP algorithm substantially improves docking results.
Keywords :
biology computing; message passing; proteins; MWIS; SCP; computational protein docking methods; distributed algorithm; enzyme-inhibitor protein complexes; high-quality feasible solution; local information; maximum weighted independent set problem; message-passing; neighboring nodes; protein folding applications; side-chain positioning; software; unbound protein structures; Algorithm design and analysis; Approximation algorithms; Clustering algorithms; Nickel; Prediction algorithms; Protein engineering; Proteins;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Decision and Control (CDC), 2013 IEEE 52nd Annual Conference on
Conference_Location :
Firenze
ISSN :
0743-1546
Print_ISBN :
978-1-4673-5714-2
Type :
conf
DOI :
10.1109/CDC.2013.6759970
Filename :
6759970
Link To Document :
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