Algorithms for structure comparison and analysis: Docking

Protein-docking is a molecular modeling problem which aims to predict, with computer science algorithms and techniques, the mutual orientation and position of two molecules forming a complex. One of the molecules is a protein, the other could be another protein, a nucleic acid chain or a smaller molecule. Many techniques are described in literature, some of which restrict the starting hypotheses in order to cut the research space and obtain a solution more efficiently, such as: (i) Geometrical shape of molecules, (ii) hydrophobicity/hydrophilicity, (iii) binding affinity calculated through scoring functions, (iv) flexibility/rigidity of the backbone.