The adhesive protein helps aquatic organisms to attach to hard and wet substratum resulting in micro and macro biofouling which reduce the performance of ships and also increase their fuel requirements. To prevent biofouling, the shipping industries use antifouling paints which contain many chemical inhibitors but these inhibitors are toxic and harmful to the environment and hence environmental friendly biocides are being investigated. Bioinformatics tools are helpful to identify new and novel compounds for human health problems. These tools can also be used to explore the possibility of proposing novel eco-friendly compounds for the prevention of biofouling and biofilm formation. An attempt has been made to study the interaction of known inhibitors and the proximal thread matrix protein and the results were presented in this paper. By comparing the binding energy values of different inhibitors, the strength of binding of different chemicals with the protein and thus the chemical having better inhibiting property were described. © 2015, Global Research Online. All rights reserved.