SUSPECT_BDQ is a user friendly web server that implements an supervised predictive algorithm for predicting effects of missense mutations in atpE which leads to resistance against Bedaquiline This tool could be useful for the rapid characterization of novel clinical variants, to help guide the effective use of bedaquiline, and to minimize the spread of clinical resistance.
The submission page for user input mutations can be accessed via the menu item Run (1) on the top bar menu. The Single Mutation (2) option allows the user to submit one single mutation for prediction. (3) A mutation code consists of a wild-type code, residue position and mutant code (using the one letter amino acid code). The residue position must be consistent with the PDB file.
The Mutation List (4) option allows the user to submit a list of single mutations to be analysed by SUSPECT_BDQ in batch. The list of single-point mutations must be input (5) by uploading a file containing the mutation codes (wild-type residue code, position and mutant residue code). The file format requires one mutation mutation per line. A sample file is also provided.
The results page for a single mutation will be shown once computations are completed in 3 different panels. On the first panel, the predicted outcome is displayed (1) alongside with the wild type environment details of the mutation being analysed (2). Individual values of all the features calcuated is displayed (3). The second panel will show the interactive 3D viewer (4), which allows user to analyse the interatomic interactions between the wild-type residue and nearby residues. Interactions can be hidden or displayed using the controls provided (5). The viewer can be manipulated using buttons at the bottom of the panel (5). SUSPECT_BDQ also allows users to analyse the interatomic interactions of the mutant with the nearby residues.
The results page for a list of single mutations will be shown once computations are completed in a single table. The predicted susceptibility profile for every single-point mutation will be displayed on a table (1). A set of controls for sorting based on columns and an input for text search are also provided. All the analysis discussed for the Single Mutation option can be analysed for each single mutation on the table through the Details button (2) of each row. Results can be downloaded as a .csv file by clicking on the Download button on the top right corner (3). The second panel will show the interactive 3D viewer (4) in which the interface residues are colored according to the susceptibility profiles. The drug molecule Bedaquiline (BDQ) is shown in yellow as ba;; and stick representation. The viewer can be customised using the controls on the top of the panel (5). A set of buttons are displayed at the bottom of the panel (6) to adjust visualisation.
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