99 co-crystallized protein-protein complexes and corresponding X-ray unbound structures for both proteins,
and 134 co-crystallized complexes and corresponding X-ray unbound structure for one protein. Sequence identity
between bound and unbound structures > 97 %.
396 co-crystallized protein-protein complexes and corresponding X-ray unbound structures for both proteins.
(Initial set of 1020 binary subunit complexes identified by the ProPairs algorithm [Krull et al. J Chem Inf Model 2015, 55:1485]
was filtered based on sequence and structure similarity criteria: sequence identity = 96%, TMscore = 0.8).
Arrays of six models (1, 2, 3, 4, 5 and 6 Å RMSD from the native structure) of each monomer in 165 protein-protein complexes selected from X-ray Bound set at 30% sequence identity. All models are obtained by I-TASSER (Zhang Lab)
Arrays of five models (with decreasing accuracy according to modeling rank) of each monomer in 171 protein-protein complexes selected from Dockground docking benchmark set 4. All models are obtained by Phyre2 (Sternberg Lab)
Arrays of five models (with decreasing accuracy according to modeling rank) of each monomer in 963 protein-protein complexes selected from GWIDD database. All models are obtained by Phyre2 (Sternberg Lab)
99 incorrect and one near-native (acceptable or better by the CAPRI criteria) docking matches generated by GRAMM scan, for each distortion level of individual protein structures from complexes in Model set 2.0.
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.