title: A Message Passing Approach to Side Chain Positioning with Applications in Protein Docking Refinement.
abstract: We introduce a message-passing algorithm to solve theSide Chain Positioning (SCP)problem. SCP is a crucial component ofprotein docking refinement, which is a key step of an important class of problems in computational structural biology calledprotein docking. We model SCP as a combinatorial optimization problem and formulate it as aMaximum 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.
authors.affiliation: Division of Systems Eng., Boston University, mohamad@bu.edu.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Moghadasi
authors.forename: Dima
authors.initials: D
authors.lastname: Kozakov
authors.forename: Artem B
authors.initials: AB
authors.lastname: Mamonov
authors.forename: Pirooz
authors.initials: P
authors.lastname: Vakili
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
authors.forename: Ioannis Ch
authors.initials: IC
authors.lastname: Paschalidis