P-glycoprotein (Pgp) is an efflux transporter that is a member of the ATP binding cassette (ABC) superfamily. The transporter is found on the apical surface of cells and hydrolyzes ATP to expel a diverse range of xenobiotics into the extracellular space. The ubiquitous expression of Pgp dramatically effects drug disposition of many therapeutics and overexpression in cancerous tumors leads to multidrug resistance. As a result, Pgp-mediated transport represents a formidable hurdle to drug development. Another complicating factor is that drug transport rates can be different between drugs of the same class. To better understand this phenomenon, we investigated the triptan drugs, eletriptan (ETT) and sumatriptan (STT), with Pgp because the transport rate of ETT is 5- to 22-fold higher than STT. Despite their structural similarity, competition experiments revealed that they occupy distinct sites on the transporter. Fluorescence experiments revealed that the drugs shift Pgp into different conformations, while NMR experiments uncovered well defined drug interactions with the transporter. With this experimental information, a simplified conformationally-driven transport model was proposed. However, to understand drug transport on a molecular level, the drug locations need to be pinpointed on the transporter. Therefore, a hybrid molecular docking software wrapper called HADDOCK-Vina was developed, which fuses HADDOCK protocols with AutoDock Vina. With the wrapper, we demonstrated that we can accurately reproduce the ligand positions of three ligand-bound X-ray crystal structures using experimental data to drive docking, as well as correct parametrization of a paramagnetic spin label. We used experimental data to drive the docking of ETT and STT onto Pgp by HADDOCK-Vina. The docking reveals distinct interactions between the drugs and Pgp, but some ambiguity still exists in their positions. Our preliminary ETT- and STT-bound models reveal the structural basis of triptan transport and demonstrates a rapid method to screen Pgp substrates for drug discovery. Future studies include incorporating a paramagnetic label onto Pgp to pinpoint drug binding sites and modeling these sites by HADDOCK-Vina.