Molecular docking means finding the

Molecular docking means finding the binding orientation of two molecules with known
structures. The binding of small molecule ligands to large protein targets is central to numerous
biological processes. The accurate prediction of the binding modes between the ligand and protein,
(the docking problem) is of fundamental importance in modern structure-based drug design. The
task of molecular docking can be divided according to the molecules being involved:
 Protein-Ligand docking
 Protein-Protein docking
Specific docking algorithms are usually designed to deal with one of these problems but not with
both (different contact area, flexibility, level of representation). Assuming the receptor structure is
available, a primary challenge in lead discovery and optimization is to predict both ligand orientation
and binding affinity.
The major techniques currently available are: molecular dynamics, Monte Carlo methods,
genetic algorithms, fragment-based methods, point complementarity methods, distance geometry
methods, tabu searches and systematic searches.