Given a starting structure and the major modes that span the conformational space of a protein, generate a set of conformations to capture the flexibility of the protein. That is, capture the most important motions by starting from the initial structure and following in the direction of the major modes. Our work is performed around the native structure, as analysis fails if we are far from the native.
We focus our analysis on HIV-1 protease, a virus protein that assists in the replication of HIV. Much work has been done in designing drugs to block its active site and thus prevent the virus from replicating. Furthermore, the size of the protease is computationally manageable but large enough to address important problems, and there is abundant data characterizing this protein on which we can validate our results.