Dockground

Unbound Docking Benchmarks

Protein-protein complexes and experimental structures of unbound components.

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How this set was generated
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Protein complexes were selected from the Bound part of Dockground with the following criteria: mean area buried ≥ 500 Å², 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.