Work

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

Year: 2012

Type: conference-paper

Abstract: 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.

Source: IEEE Conference on Decision and Control (CDC)

DOI: 10.1109/cdc.2012.6426600

Authors: Mohammad Moghadasi, Dima Kozakov, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis

Institution: Boston University

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Institute of General Medical Sciences

Awards: A multistage approach to protein-protein docking, Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energ, G700947639