Current approaches to enzyme specificity focus on the identification of consensus sequences from combinatorial chemistry libraries or phage display. These synthetic substrates can also be used as sensitive probes for the molecular environment of the enzyme specificity sites to determine how they contribute to recognition in the transition state. Libraries constructed to include all relevant species for a site-specific analysis contain a relatively small number of substrates and provide quantitative information on the energetics of recognition that can be exploited in studies of structure-function relations and rational drug design. We have constructed a library of substrates carrying substitutions at P1, P2, and P3 to probe the response of the specificity sites S1, S2, and S3 of thrombin. The library has been used to identify differences between the anticoagulant slow and procoagulant fast forms of thrombin and the structural origin of the effects. The results also offer new guidelines for the design of active-site inhibitors of thrombin.