Graphical models for protein structure: Difference between revisions

Revision as of 05:58, 21 July 2010

Revision as of 15:18, 17 August 2010

Line 1:

{{orphanOrphan|date=June 2010}}

{{nofootnotes|date=June 2010}}

{{orphan|date=June 2010}}

[[Graphical model]]s have become powerful frameworks for [[protein structure prediction]], [[protein–protein interaction]] and [[free energy]] calculations for protein structures. Using a graphical model to represent the protein structure allows us to solve many problems including secondary structure prediction, protein protein interactions, protein-drug interaction, and free energy calculations.

Line 20:

:<math>p(X = x|\Theta) = p(X_b = x_b)p(X_s = x_s|X_b,\Theta), \,</math>

where <math>\Theta</math> represents any parameters used to describe this model, including sequence information, temperature etc. Frequently the backbone is assumed to be rigid with a known conformation, and the problem is then transformed to a side-chain placement problem. The structure of the graph is also encoded in <math>\Theta</math>. This structure shows which two variables are conditionally independent. As an example, side chain angles of two residues far apart can be independent given all other angles in the protein. To extract this structure, researchers use a distance [[threshold]], and only pair of residues which are within that threshold are considered connected (i.e. have an edge between them).

Given this representation, the probability of a particular side chain conformation ''x''_''s'' given the backbone conformation ''x''_''b'' can be expressed as