Dockground

Protein-protein complexes and experimental structures of unbound components.

X-ray unbound benchmarks

• Selection Criteria
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  DOCKGROUND Help

  Representative datasets in the easy mode are generated using the following constraints:
  

  - Sequence identity* between bound and unbound structures > 97%

  - Sequence identity between complexes < 30% ¹

  - Delete homomultimers (sequence identity between chains < 70%)

  - Delete crystal packing complexes and structures in wrong format.
  
  

  Legend

  
  

  * Using BLAST to calculate the sequence identity.

  ¹ The sequence identity is used to discard redundant co-crystallized structures.

• Download set 1 (15.6MB, 92 complexes)
• Download set 2 (30.4MB, 242 complexes)
• Download set 3 (31.0MB, 233 complexes)
• Download set 4 (50.7MB, 396 complexes)

Simulated unbound benchmark

• Download set 1 (92.9MB, 3,205 complexes)
• Select proteins from set 1
• How this set was generated
  x

  DOCKGROUND Help

  Protein complexes were selected from the Bound part of Dockground with the following criteria: mean area buried ≥ 500 Ų, include alternative binding modes, homo/hetero n-mers, and oligomers, and the redundancy cutoff 97%. The resulting set contained 1918 protein-protein complexes. Program Profix from the Jackal package (http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software) was used to build the disordered residues and missing atoms. To speed up the calculations, we chose the Langevin Dynamics (LD) simulation in CHARMM (CHARMM22 force field) performed on each bound structure without its interacting partner. Prior to LD simulation, the initial structures from PDB files were minimized (by 50 steps of steepest descent minimization followed by 500 steps of adopted basis Newton-Raphson minimization). In the simulation, the backbone atoms of helices and strands were constrained with a force constant of 5 kcal/mol, the temperature was set to 309.6 K, the bond lengths were fixed using shake with tolerance 1.0E-8, the friction force fbeta was 5.0, and the time of simulation was 1ns, with 100 snapshots saved. The structure with the largest all atoms RMSD from the bound structure was designated as the simulated unbound structure.