Molecular Docking

Molecular docking is a computational procedure that attempts to predict non-covalent binding of macromolecules or, more frequently, of a macromolecule (receptor) and a small molecule (ligand) efficiently, starting with their unbound structures, structures obtained from MD simulations, or homology modelling, etc. The goal is to predict the bound conformations and the binding affinity.

The prediction of binding of small molecules to proteins is of particular practical importance because it is used to screen virtual libraries of drug-like molecules in order to obtain leads for further drug development. Docking can also be used to try to predict the bound conformation of known binders, when the experimental holo structures are unavailable.1

One is interested in maximising the accuracy of these predictions while minimising the computer time they take, since the computational resources spent on docking are considerable.

Molecular docking has become an increasingly important tool for drug discovery. In this review, we present a brief introduction of the available molecular docking methods, and their development and applications in drug discovery. The relevant basic theories, including sampling algorithms and scoring functions, are summarised. The differences in and performance of available docking software are also discussed. Flexible receptor molecular docking approaches, especially those including backbone flexibility in receptors, are a challenge for available docking methods. A recently developed Local Move Monte Carlo (LMMC) based approach is introduced as a potential solution to flexible receptor docking problems. Three application examples of molecular docking approaches for drug discovery are provided.

Autodock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared to the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multi-core machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.