BENCHMARK VERSION 3.0

Protein structures for Benchmark 2.0 are located in Benchmark_2 directory, 
the updated protein structures for Benchmark 3.0 are located in Benchmark_3_updated directory and,
the updated protein structures for Benchmark 4.0 are located in Benchmark_4_updated directory.

FILE NAMING FORMAT

The file name format of the benchmark structure files consists of 12 characters:
Characters	
      1-4: Complex PDB Code*
	5: '_'
	6: 'l' if ligand, 'r' if receptor
	7: '_'
	8: 'u' if unbound constituent, 'b' if bound constituent
     9-12: '.pdb' (file extension)

*The Complex PDB Code is the PDB code of the structure from which the bound receptor and ligand are obtained.  In the cases of 1QFW and 2QFW both cases are obtained from the 1QFW PDB file, thus the creation of the PDB name 2QFW for the purpose of uniqueness was necessary.  2QFW is not a valid PDB code, and is only used in this benchmark.  If at any time 2QFW does become a valid PDB code for the Protein DataBank, the case known as 2QFW shall be renamed.

*Each unbound strcuture was superimposed onto the corresponding bound complexe. This fact may cause biased docking results if docking algorithm is sensitive to initial position of receptor/ligand.  Users can avoid the possible biased docking results by randomizing the unbound strcutre positions.

*2QFW is renamed to 9QFW since PDB code 2QFW is assigned to a PDB entry.

*1TFH contains two chains, A and B, for the same protein with an identical sequence. The two chains have different missing residues. 
 1TFH chain A is used as a unbound constituent of 1AHW and 1TFH chain B is used as as unbound constituent of 1JPS and 1FAK. 
 To make them consistent, we added 1JPS_l_u.pdb.2 and 1FAK_l_u.pdb.2 using 1TFH chain A for the downloadable files.
