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Abstract: Understanding the differences between murine (m) and human (h) proteinase 3 (PR3) and neutrophil elastase (NE) is crucial for the interpretation of in vivo studies of inflammatory processes. We built structural models of mPR3 and mNE and analyzed their surface properties. We performed molecular dynamics (MD) simulations on several enzyme–peptide complexes to investigate their interaction patterns. The analysis of trajectories confirms that murine and human complexes have different interaction patterns with peptidic substrates. We provide a map of the binding sites of the murine proteases and suggest sequence motifs that we predict to be specific for mPR3 or mNE. [Copyright &y& Elsevier]