Application of Computational (in silico) methods are widely applied in drug discovery. In drug discovery process, recognition of the appropriate drug target is the first and leading task. These targets are biomolecules which mainly include DNA, RNA and proteins (such as receptors, transporters, enzymes and ion channels). Rationale of such targets is necessary to exhibit a sufficient level of ‘confidence’ and to get knowledge of their pharmacological relevance to the disease under investigation. Cyperus rotundus is one of the promising medicinal plant having anti-arthritic activity. This study is to illustrate some of the in silico methods applied for the validation of isolated molecules from the plant. This article aims to bring out the new technique in drug discovery.