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Computational models of cells, tissues and organisms are necessary for increased understanding of biological systems. In particular, modeling approaches will be crucial for moving biology from a descriptive to a predictive science. Pharmaceutical companies identify molecular interventions that they predict will lead to therapies at the organism level, suggesting that computational biology can play a key role in the pharmaceutical industry. We discuss pharmaceutically-relevant computational modeling approaches currently used as predictive tools. Specific examples demonstrate how companies can employ these computational models to improve the efficiency of transforming targets into therapies.