This article is part of the supplement: Proceedings of the European Conference on Computational Biology (ECCB) 2008 Workshop: Annotations, interpretation and management of mutations (AIMM)
Research
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease
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* Corresponding authors: Ronald M Levy ronlevy@lutece.rutgers.edu - Alexandre V Morozov morozov@physics.rutgers.edu
1 BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway NJ 08854, USA
2 Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway NJ 08854, USA
3 Department of Physics and Astronomy, Rutgers, the State University of New Jersey, 136 Frelinghuysen Road, Piscataway NJ 08854, USA
BMC Bioinformatics 2009, 10(Suppl 8):S10 doi:10.1186/1471-2105-10-S8-S10
Published: 27 August 2009Additional files
Additional File 1:
Mutation frequencies for selected positions in the HIV protease as a function of the number of PIs the patient was exposed to. Data is shown for residues 10 (black, solid line), 54 (red, solid line), 90 (green), 71 (blue), 46 (orange), 77 (black, dashed line), and 35 (red, dashed line).
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Additional File 2:
Predicted vs observed probabilities for the 210 mutational states of the ten-residue group 20-32-46-48-53-54-58-74-82-90 in HIV protease for the PI2+ cohort. Mutational states that were unobserved in the database and would have an observed probability maximum likelihood estimate of zero are not shown. The black dots correspond to the best-fit independent model, the red dots correspond to the best-fit pair-term model (Equation 11), and the green dots correspond to the best-fit three-body model (Equation 12). The solid line of slope 1 corresponds to perfect agreement of the predicted data with the observed, which would be obtained if all higher-order terms were included.
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Additional File 3:
Scatterplot of distance vs λij parameters estimated using I and J values of ± 1 as described in the Methods for the 15-residue group 10-20-33-36-46-54-55-63-71-73-74-82-84-90-93 in the PI2+ cohort. The value along the y-axis is the closest distance between any two heavy atoms of the two residues based on the crystal structure of wild type protease (PDB ID 1PRO).
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