Docking simulation methods

II. Docking simulation methods These are slower than the matching one, study the ligand outside the protein and randomly explore translations, orientations and conformations until an ideal site is found. 

Molecular dynamics simulation methods are currently the most popular approaches. This method is for the analysis of protein flexibility and dynamic properties of molecular systems. With respect to docking, these simulations could provide a realistic view of the docking process, however, these calculations are still out of reach. Therefore, dynamical simulations during the docking process are limited to the protein-ligand complexes. Molecular dynamical simulations are often... 

Pak Y, Wang S. Application of a molecular dynamics simulation method with a generalized effective potential to the flexible molecular docking problems. J Phys Chem B 2000 104 354-359. 

There are still many unsolved problems in computational chemistry and, as discussed, many of them are not new. We still need a method for the quick and accurate calculation of free energies, and we need to understand the limits on the accuracy of any predictive methods. More broadly, what confidence limits can we put on any given prediction from any given level of theory For virtual screening, what are the most important terms left out of the standard docking functions, and indeed higher simulation methods Can we imagine a set of widely accepted well-validated model systems and benchmarks, both for experiment and theory ... 

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