Natural products serve as an invaluable source of chemical structures for drug development. However, the labor-intensive experimental steps and the requirement for large amounts of input (natural extract) restrict the implementation and success of drug discovery projects based on natural products. Consequently, we propose the establishment of the NP3 platform. This computational platform aims to expedite the process of identifying new bioactive natural products and their binding sites on target proteins. It does so based on three unconventional experimental inputs: i) the electronic density of the inhibitor, observed from protein crystallography data; ii) mass fragmentation data, obtained from LC-MS/MS analysis; iii) the biological activity of the chemical samples. These experimental data are derived from unpurified natural product samples at the beginning of the discovery process. Their automated processing via the NP3 platform is expected to accelerate the discovery phase of bioactive natural products, thereby facilitating the development of new drugs derived from natural products.