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It has been demonstrated that, in vivo, a hemorrhagic P-I SVMP hydrolyzes type IV collagen and perlecan to a higher extent than a non-hemorrhagic P-I SVMP. In order to gain further insights on this phenomenon, the protein-protein docking approach was used to analyze the mode of interaction of four different SVMPs with two different domains of perlecan and two different domains of type IV collagen. The hemorrhagic SVMPs are BaP1 and acutolysin-A, and the non-hemorrhagic ones are BmooMPα-I and H2-proteinase. In general, hemorrhagic SVMPs could form catalytic complexes with the triple-helical domain of type IV collagen, and with laminin-like globular domain 3 and immunoglobulin (IG)-like domain of perlecan. It is hypothesized that the formation of these catalytic complexes may explain the differences observed in vivo in the degradation of collagen IV and perlecan. Moreover, our results suggest that there are differences in the area and volume of the active site cleft between hemorrhagic and non-hemorrhagic P-I SVMPs, since the latter present a larger volume and area. We suggest that this structural characteristic favors the interaction with substrates; nevertheless, at the same time, it could decrease the probability to achieve a stable complex. However, these results should be confirmed by means of experimental and bioinformatics assays.