Although the small molecule herbicide binding effects and inhibition of AHAS catalytic activity is known , and x-ray structures exist of AHAS with and without these 5 classes of herbicides (primarily in Arabidopsis Thaliana and Saccharomyces cerevisiae), the computational molecular analysis of inhibition of the herbicide binding site is not complete, particularly in protein-ligand docking studies. In addition, x-ray structures are an entropically frozen state that does not guarantee modeling of thermal biologic conditions. In general the question as to whether a plant is resistant to an inhibitor is unaccompanied by any x-ray structure information at all. The use of computational molecular modeling techniques can aid in the search/selection of point mutations to improve crop performance via resistance factors, including quantification in dose. Molecular herbicide design and crop improvement can benefit substantially.