			BENCHMARK 1.0

This is the README file for release 1.0 of protein-protein docking
benchmark. It contains both the individually crystallized receptor and
ligand PDBs and the co-crystallized complex PDBs for testing protein
docking algorithms. The current version contains 59 test cases: 22
enzyme-inhibitor complexes, 19 antibody-antigen complexes, 11 other
complexes, and 7 difficult test cases. 31 of the test cases, for which the
unbound structures of both the receptor and ligand are available, are
classified as follows: 16 enzyme/inhibitor, 5 antibody/antigen, 5 others
and 5 difficult. Detailed description can be found in benchmark.pdf. Please
reference "Chen R., Mintseris J., Janin J., & Weng Z., A Protein-Protein
Docking Benchmark, Proteins (in press)".  

This distribution includes 4 following directories. 
unbound_pdb:              contains individually crystallized receptor and
                          ligand PDBs (unbound/unbound or unbound/bound),
			  after they have been superposed onto the
			  corresponding molecules in a co-crystallized 
                          protein complex.

unbound_interface_ca:     contains the interface CA atom coordinates extracted
                          from thosed files in unbound_pdb.

co_crystal_pdb:           contains the receptor and ligand parts of the
                          co-crystallized protein complexes.

co_crystal_interface_ca:  contains the interface CA atom coordinates extracted
                          from thosed files in co_crystal_pdb.

More information can be found in the README files in each directory.

There are several ways to evaluate your docking predictions. Two of them
are RMSD and interface RMSD. For RMSD evaluation, use superposed receptor
and ligand PDBs in unbound_pdb to predict complex structures, and compare
your predictions with the corresponding experimental complex structures in
co_crystal_pdb (random rotation is needed inside your protein docking
program). For interface RMSD evaluation, use the transfomation matrix from
your docking program to transform interface files in unbound_interface_ca
and then compare with corresponding experimental interface files in
co_crystal_interface_ca. Normally, if the superposition only involves the
receptor, 5 angstrom is a good RMSD criteria for a hit. If the
superposition involves the whole complex, 2.5 angstrom is a good criteria
for a hit.
