BT cotton is a variety of cotton that genetically modified which contains a gene of Bacillus thuringiensis (BT), which is foreign to its genome. Different BT strains produce different Cry-proteins and there are hundreds of known strains. Major problem of today is that several insects developing resistance against BT cotton plant or there is no effect of BT toxic protein on insect control. In this context, this book addresses the problem using bioinformatics tools. Before developing BT cotton variety the most important thing is to check the binding efficiency of toxin protein to specific insect med gut membrane, development of resistance or delay resistance insect to BT variety reduce by matching med gut membrane structure and effective toxin protein with use of many protein-protein docking software. Obtainable results give idea to effectiveness or play key role in design variety of BT cotton seed.