  Each and every biological function in living organism happens as a result of
protein-protein interactions.The diseases are no exception to this. Identifying
one or more proteins for a particular disease and then designing a suitable
chemical compound (known as drug) to destroy these proteins has been an
interesting topic of research in bio-informatics. In previous methods, drugs
were designed using only seven chemical components and were represented as a
fixed-length tree. But in reality, a drug contains many chemical groups
collectively known as pharmacophore. Moreover, the chemical length of the drug
cannot be determined before designing the drug.In the present work, a Particle
Swarm Optimization (PSO) based methodology has been proposed to find out a
suitable drug for a particular disease so that the drug-protein interaction
becomes stable. In the proposed algorithm, the drug is represented as a
variable length tree and essential functional groups are arranged in different
positions of that drug. Finally, the structure of the drug is obtained and its
docking energy is minimized simultaneously. Also, the orientation of chemical
groups in the drug is tested so that it can bind to a particular active site of
a target protein and the drug fits well inside the active site of target
protein. Here, several inter-molecular forces have been considered for accuracy
of the docking energy. Results show that PSO performs better than the earlier
methods.
