Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

Background: Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins. Results: Here we report a new implementation of the CM method with an added set of selection rules (filters). The parameters of the algorithm were optimized against fifteen high resolution crystal structures with optimization criterion that maximized the confidentiality of the predictions. The optimization resulted in a true positive ratio (TPR) of 0.08 for the CM without filters and a TPR of 0.14 for the CM with filters. The protocol was further benchmarked against 65 high resolution structures that were not included in the optimization test. The benchm...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Petras J. Kundrotas, Emil Alexov
• Keywords: Amino Acid Sequence, Amino Acids, BMCBI 2006, Selection Rules