International Journal of Pharmacy and Drug Research. Volume 2, Number 1 (2013), pp. 1-10 © Research India Publications http://www.ripublication.com/ijpdr.htm Comparitive Study of Various Ebola Virus Vp40 Strains with Modelling and Docking Studies to Treat Ebola Virus Infection Jigar Patel, Yashodhan Chipkar and Afaque Momin Department of Bioinformatics, GNIRD, Guru Nanak Khalsa College, Mumbai, India. Email:-Jigar.patel3112@gmail.com. Abstract: Computer aided drug design is one of the powerful toolsfor discovering new drug leads against important targets. The Ebolavirus is a naturally resistant virus to various antibiotics, and there is noproper treatment for infection caused by this pathogen, hence there is a need for new drugs and approaches tocombat the life threatening infection caused by Ebola virus. The viral protein vp40 is capable of eliciting protective immuneresponses to EBOV. The various functions of these proteins in pathogenesis suggested them as potential drugtargets to control EBOV infections. In this work, the VP 40 protein sequences were selected from different countries and a multiple sequence analysis was performed to find out the homology between sequences. Three sequences were chosen which were homolog’s of each other and the leads were designed which would act on all the three strains. New leads were designed which scored well when docked against targets. The drug lead molecules were evaluated for their drug likeness using “Lipinski rule of five”. The identification of appropriate drug lead molecules against these proteins has lead to a successful drug candidate against Ebola virus infection. Keywords: Ebola virus, Hemorrhagic fever, Computer aided drug design, multiple sequence analysis, Lipinski rule of five. INTRODUCTION: Ebola virus is a deadly pathogenic virus. It is classified under filoviridea family. It was first identified in Africa in1976 in The Democratic Republic of Congo.