Dhanvantari is a pipeline to incorporate novel scientific methods and highly efficient algorithms along with combining principles of Chemistry and Biology with Information Technology for target directed Drug Designing. The pipeline covers all the aspects from genome through genes, proteins, active site to a final proposed lead like compound. The pipeline is being tested for viral genomes and estimated average time taken is 3 hrs to reach from a viral genome to its potential leads.The automation at every step facilitates the naive users to use the pipeline with set default parameters which would render scientifically significant output in most of the disease cases. Also the users are allowed to do any required changes in the parameter set in the pipeline as per their need. In short, the pipeline bridges the gap between an unknown disease to its potential treatment.