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Natural products have been the source of treatment for various human diseases from time immemorial. Interests in natural product‐based scaffolds for the discovery of modern drugs have grown in recent years. However, research on exploring the traditional medicinal systems for modern therapeutics is severely limited due to our incomplete understanding of the therapeutic mechanism of action. One possible solution is to develop computational approaches, based on ligand‐ and structure‐based screening tools, for fast and plausible target identification, leading to elucidation of the therapeutic mechanism. In the present work, we present two methods based on shape‐based and pharmacophore search to predict targets of natural products and elucidate their mechanism, and to identify natural product‐based leads. These methods were tested on an in‐house developed database of medicinal plants that include information from a largely unexplored North‐East region of India, known as one of the twelve mega biodiversity regions. However, depending on the choice of the lead molecules, any existing databases can be used for screening. MedPServer is an open access resource available at http://bif.uohyd.ac.in/medserver/.

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