This protocol describes a method for detection of bacterial proteins involved in efflux mediated antibiotic resistance (ARE) and their sub-families as described in the research paper entitled "BacEffluxPred: A two-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins” published in Scientific Reports. BacEffluxPred is a support vector machine based two-tier prediction method, that can be used for the detection of efflux proteins responsible for antibiotic resistance in bacteria and to identify the families to which it belongs. The overall prediction cycle includes three important steps:
1) The query protein is presented to the prediction algorithm.
2) If the query protein would be predicted to be a non-ARE protein, the prediction would stop at tier-I.
3) If the query protein would be predicted as an ARE protein at the tier-I, the query protein would be forwarded to tier-II for ARE family prediction.
By using these steps it is possible to generate the models that can be used on proteomic data to predict whether the given data have potential ARE proteins or not if yes it will further classified into their following families. This is the first in-silico tool for predicting bacterial ARE proteins and their families and it is freely available as both web-server and standalone versions at http://proteininformatics.org/mkumar/baceffluxpred/