Structural alignment of compounds

Question

[Janeeta Raja]

Is there any algorithm for structural alignment of compounds (using pdb files)? or which algorithms are used for finding structurally similar compounds by using which parameters as in Pubchem compounds and in chemicalize org?

Answer 1

[Pappu]

Look zinc.docking.org

[Janeeta Raja]

Thanks. But I want the strategy and algorithm behind structural similarity searches.