Computational protocol: Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance

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Protocol publication

[…] Structure modelling of the D7r2 protein was carried out using the crystal structure of D7r4 protein bound to serotonin (PDB code 2qeh; []) as a template. HHpred [, ] was used to align the target and template, which shared 32% sequence identity, producing an alignment covering residues 3–146 of the D7r2 protein. MODELLER [] was used to generate 40 models from this alignment and DOPE scores [] used to select the best model.PyMOL ( was used for manual positioning of bendiocarb into D7 protein structures. Automated small molecule docking was then done at the ROSIE/Rosetta [, ] server. PDBSUM [] was used to obtain a precalculated definition of the cavity shape and volume of the D7r4 crystal structure, and ProFunc [] used for similar calculations on model structures. [...] GraphPad Prism version 5.04 for Windows statistical software (GraphPad Software) was used to perform Fisher’s exact, Mann-Whitney and Spearman tests for statistical significance. The lower and limits of the 95% confidence interval for a proportion were calculated using VassarStats ( […]

Pipeline specifications

Software tools HHPred, MODELLER, PyMOL, ROSIE, ProFunc, VassarStats
Applications Miscellaneous, Protein structure analysis
Organisms Anopheles gambiae
Chemicals Serotonin