Most ligand-protein docking programs, including GOLD, are not suitable for docking proteins to other proteins because the problems that must be solved when docking proteins are sufficiently different from those when docking ligands. In particular GOLD requires a distinct concave binding site to be defined, whereas many protein binding interfaces do not have strong concavity.

There are many docking programs available which have been designed specifically for protein-protein docking, including GRAMM-X, HADDOCK, Hex, zdock, RosettaDock or ClusPro.

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