This decoy set is provided for assesment of scoring functions for
protein-protein docking.

There are 100 structures in the set.

The first is the experimental crystal structure.

The next 3 are close models, selected from our rigid-body docking
simulations (which also includes an electrostatic binary filter).
These all have a RMSD of less than 7 Angstroms from the experimental
crystal structure.
This RMSD is calculated over the interface C-alpha atoms of the smaller
component of the complex, the larger component having been superposed by
C-alpha atoms onto the experimental structure.
The interface is defined for each component of the complex as consisting
of any residue which has at least one atom within 10 Angstroms of any
atom in the other component. 
These 3 close models also exhibit at least 25% of the residue contact
pairs across the interface that are observed in the experimental crystal
structure.  A pair is considered to exist across the interface if two
residues on different sides of the interface have atoms within
4.5 Angstroms of each other.

The remaining 96 are decoys, grouped into bins of 3 for each 1 Angstrom
RMSD range.
The lowest range is from 9 to 10 Angstroms, the highest from 40 to 41,
making a total of 32 bins. 
These decoys were selected by binning the much longer list of possible
docked complexes generated by our simulations and choosing as decoys
the 3 in each bin with the highest surface complementarity scores. 

The values are in a file, with columns giving the values;

complex_number  rmsd  surface_complementarity  percentage_correct_pairs


http://www.bmm.icnet.uk/docking/

Gidon Moont
May 2001
