It is as powerful as the docking method, and is always more efficient than docking methods.
Binding modes of representative structures were analyzed using the docking method to explain the observed disparity in HDAC1 inhibitory activities.
The docking method is similar to that previously employed for class I MHC [36], with the main difference being the use of modified peptide backbone constraints.
The performance of the docking method was evaluated by redocking the crystal ligands into the assigned active site of the respective enzymes to determine the root mean square deviation (RMSD) values.
The docking method was performed using a two-step process of rigid-body Monte Carlo searching and parallel optimization of the backbone displacement and side-chain conformations.
Docking of N-TIMP-3 with the ADAM17 component from the N-TIMP-3 ADAM17 complex (PDB code 3CKI) was first performed to validate the dockiN-TIMP-3 ADAM17
The docking method was able to reproduce the experimentally bound conformation of ligand in the active site with an RMSD of <2 Å.
Right now, I'm completely obsessed with the Dock Method, which is this thing where you work on the docks for a few hours, tossing cargo into shipping holds, and they pay you $6.75 an hour.
The large majority of the docking methods are ab initio methods, designed towards the latter class of complexes, although experimental data can often be incorporated to restrict the search space.
This suggests that the docking methods used here are useful for the purpose we describe.
