Refining intra-protein contact prediction by graph analysis

Background: Accurate prediction of intra-protein residue contacts from sequence information will allow the prediction of protein structures. Basic predictions of such specific contacts can be further refined by jointly analyzing predicted contacts, and by adding information on the relative positions of contacts in the protein primary sequence. Results: We introduce a method for graph analysis refinement of intra-protein contacts, termed GARP. Our previously presented intra-contact prediction method by means of pair-to-pair substitution matrix (P2PConPred) was used to test the GARP method. In our approach, the top contact predictions obtained by a basic prediction method were used as edges to create a weighted graph. The edges were scored by a mutual clustering coefficient that identifies highly connected graph regions, and by the density of edges between the sequence regions of the edge nodes. A test set of 57 proteins with known structures was used to determine contacts. GARP improve...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Milana Frenkel-Morgenstern, Rachel Magid, Eran Eyal, Shmuel Pietrokovski
• Keywords: Basic Prediction, BMCBI 2007, Contacts, Prediction