Fig. 4

An example of binding mode reconstruction. The binding mode of the compound brivudine binding to the target deoxynucleoside kinase was reconstructed with an RSS = 0.66. On the left, the original binding mode of the complex (2VQS:BVD:C:1210) is represented and on the right the reconstructed binding mode based on the fragments. Both fragments have a relatively high binding mode conservation with an mTIS of 0.88 and 0.63. The interactions look almost alike in both cases, except for the water bridge in Fragment I and the salt bridge and the hydrogen bond in Fragment II