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- "bound perturbations": from perturbations of the bound complex structure (with native sidechains removed and rebuilt from rotamers). 1000 decoys for each of 54 targets. bound_perturb.tgz (3.3G)
- "unbound perturbations": from perturbations of the unbound component structures which were superimposed on the bound backbones (again, with sidechains removed and rebuilt). 1000 decoys for each of 54 targets. unbound_perturb.tgz (3.3G)
- "global": top 200 structures from global searches starting from unbound starting structures with rebuilt sidechains. These sets may or may not have near-native decoys. 200 decoys from each of 54 targets. unbound_global.tgz (677M)
Docking benchmark set from http://zlab.bu.edu/~rong/dock/benchmark.shtml
- docking partners are separated by TER lines. Multiple chains in the same docking partner (e.g. heavy and light chains of an antibody) will NOT have a TER line between them.
- rms and score values are tabulated in the score files (*.fasc) in columns 3 and 2, these should match the points shown in Figs 3-5 of the JMB paper.
- natives have been taken from Chen's benchmark set, stripped of any residues with missing backbone atoms, and combined with the TER convention described above.
- Score files are missing from unbound global runs tarfile above, get them instead here: unbound_global.scores.tar
- Number of correct contacts has been calculated for unbound globals for our largest clusters: unbound_global.contacts.txt
- Maps between the residue numbering in bound and unbound decoys: maps.tar
- Note that 1BVK only has 110 decoys in the unbound_global set.
- Unbound_global contact files: unbound_global.contacts.tgz
- Unbound_perturb contact files: unbound_perturb.contacts.tgz
- Also, for reference, PDB files of the co-crystals, trimmed to the relevant residues and with TERs added appropriately to match the decoys: co_prepped.tgz