Strategic collaborations are critical to the success of efforts aimed at discovering new drugs and therapies in the biopharmaceutical industry. These collaborations aim to leverage domain expertise, asymmetries in production costs and/or capabilities to improve efficiency. Despite increasing collaborations, the biopharmaceutical industry lacks a structured guideline for choosing contracts. We present contract models with effort-based formulations that capture the key characteristics of biopharmaceutical operations and analyse incentive mechanisms such as fixed payment, revenuesharing, risk-sharing, and cost-sharing in biopharmaceutical collaborations. We show that traditional incentive schemes do not achieve supply chain coordination, although they are commonly used in the industry. We introduce a new contract model called fee-for-effort-and-output contract that encourages the parties to exert higher efforts by offering discounts on their operating costs, and show that this contract achieves coordination with an appropriate selection of contract parameters. We also investigate the efficiency of noncoordinating contracts with traditional incentive schemes and identify the capability and cost structures under which they achieve the highest efficiency possible, to both determine the next-best alternatives and explain their popularity in practice.