Benchmark

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This benchmark is a collection of distinct protein docking test cases. It includes individually crystallized receptor and ligand PDBs and the co-crystallized complex PDBs for testing protein docking algorithms.

Immune Recognition:

• TCR Docking Benchmark: Includes 20 test cases of T cell receptors binding peptide/major histocompatibility complexes. Available here
  

• Benchmark 4.0: Featuring 176 test cases: 123 Rigid-body, 29 Medium, and 24 Difficult. Available here (updated 7/2012).
  Reference for Benchmark 4.0: Hwang, H., Vreven T. Janin, J. and Weng, Z. Protein-Protein Docking Benchmark version 4.0, Proteins. 78(15):3111-4
• Benchmark 3.0: Featuring 124 test cases: 88 Rigid-body, 19 Medium, and 17 Difficult.
  Reference for Benchmark 3.0: Hwang, H., Pierce, B., Mintseris, J., Janin, J. and Weng, Z. Protein-Protein Docking Benchmark version 3.0, Proteins. 73(3):705-709
  
• Benchmark 2.0: Featuring 84 test cases: 63 Rigid-body, 13 Medium, and 8 Difficult.
  Reference for Benchmark 2.0: Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005), Protein-Protein Docking Benchmark 2.0: an update, Proteins 60(2), 214-216.
  
• Benchmark 1.0: It includes 59 test cases: 22 enzyme-inhibitor complexes, 19 antibody-antigen complexes, 11 other complexes, and 7 difficult 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. The list of PDB IDs can be found in table 1 of the reference. To download cleaned-up PDB files, click benchmark1.0.tar.gz.
  Reference for Benchmark 1.0: Chen R, Mintseris J, Janin J, Weng Z (2003) A Protein-Protein Docking Benchmark, Proteins Proteins 52: 88-91.
  
• Benchmark 0.0: It includes 54 test cases: 22 enzyme-inhibitor complexes, 16 antibody-antigen complexes, 10 other complexes, and 6 difficult cases. 29 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, 4 others and 4 difficult. The list of PDB IDs can be found here. To download cleaned-up PDB files, click benchmark0.0.tar.gz.
  Reference for Benchmark 0.0: Chen R, Weng Z (2002) Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics. Proteins 47, 281-294..