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A message passing approach to Side Chain Positioning with applications in protein docking refinement

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6 Author(s)
Moghadasi, M. ; Div. of Syst. Eng., Boston Univ., Boston, MA, USA ; Kozakov, D. ; Mamonov, A.B. ; Vakili, P.
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We introduce a message-passing algorithm to solve the Side Chain Positioning (SCP) problem. SCP is a crucial component of protein docking refinement, which is a key step of an important class of problems in computational structural biology called protein docking. We model SCP as a combinatorial optimization problem and formulate it as a Maximum Weighted Independent Set (MWIS) problem. We then employ a modified and convergent belief-propagation algorithm to solve a relaxation of MWIS and develop randomized estimation heuristics that use the relaxed solution to obtain an effective MWIS feasible solution. Using a benchmark set of protein complexes we demonstrate that our approach leads to more accurate docking predictions compared to a baseline algorithm that does not solve the SCP.

Published in:

Decision and Control (CDC), 2012 IEEE 51st Annual Conference on

Date of Conference:

10-13 Dec. 2012