Graphical Models of Residue Coupling in Protein Families

Abstract-- Many statistical measures and algorithmic techniques have been proposed for studying residue coupling in protein families. Generally speaking, two residue positions are considered coupled if, in the sequence record, some of their amino acid type combinations are significantly more common than others. While the proposed approaches have proven useful in finding and describing coupling, a significant missing component is a formal probabilistic model that explicates and compactly represents the coupling, integrates information about sequence, structure, and function, and supports inferential procedures for analysis, diagnosis, and prediction. We present an approach to learning and using probabilistic graphical models of residue coupling. These models capture significant conservation and coupling constraints observable in a multiply-aligned set of sequences. Our approach can place a structural prior on considered couplings, so that all identified relationships have direct mechani...

• Type: Journal
• Year: 2008
• Where: TCBB
• Authors: John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg
• Keywords: Coupling, Graphical Models, Residue Coupling, TCBB 2008