Docking
Knegtel et al J Comput Aided Mol Des 1999 13:167-83 Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors.
A set of 32 known thrombin inhibitors representing different chemical classes has been used to evaluate the performance of two implementations of incremental construction algorithms for flexible molecular docking: DOCK 4.0 and FlexX 1.5. Both docking tools are able to dock 10-35% of our test set within 2 A of their known positions.
Liu M, Wang S J Comput Aided Mol Des 1999 Sep;13(5):435-51 MCDOCK: a Monte Carlo simulation approach to the molecular docking problem. The root-mean-square (rms) of atoms of the ligand between the predicted and experimental binding modes ranges from 0.25 to 1.84 A for the 19 test cases.