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Figure 3 | BMC Genomics

Figure 3

From: How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics

Figure 3

Low-energy catB-heparin complexes Docking calculations were performed in two steps: firstly a blind docking calculation with grid spacing of 0.498Å, which revealed the two positive sites in catB surface as preferential heparin binding sites. Subsequently a more precise calculation were performed using a grid (spacing of 0.202 Å) centered in each site. A) Clustering analysis of 100 low-energy docking results for the first run using a 2 Å RMS deviation clustering criteria. B) Visualization of the low energy complexes obtained after the second run for each site. Inset: Enlarged view of the lowest-energy complex selected for MD simulations.

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BMC Genomics

ISSN: 1471-2164

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