Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations
Figure 5
Flowchart of the modeling process.
The procedure starts with a biased tCONCOORD sampling that takes the apo conformation and the radius of gyration of the target structure as input. An ensemble of 1000 conformations is generated and, after energy minimization, RMSD clustering and Rosetta refinement, ranked according to the ddfire scoring function. The best 50 conformations were subjected to a tCONCOORD-based sidechain resampling protocol that generates 100 conformations from each input structure with fixed backbone. Afterwards the ligand is docked into each of the 5000 conformations and the 50 best scoring solutions were subjected to molecular dynamics refinement protocol, consisting of 50 ps position restrained MD, followed by 2 ns free simulation and 200 ps simulated annealing. From those models that remained in a closed conformation (close to the holo radius of gyration) another ensemble was generated and subjected to a second refinement cycle. The best models were taken and initial docking poses generated with VINA and refined using the RosettaLigand protocol. The final ranking was carried according to the RosettaLigand score.